Technical Aspects of Integrating Water Quality Science in Freshwater and Coastal Environments

Transcription

1 Technical Aspects of Integrating Water Quality Science in Freshwater and Coastal Environments September 2016 Technical Report 2016/039

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3 Technical aspects of integrating water quality science in freshwater and coastal environments September 2016 Technical Report 2016/039 Auckland Council Technical Report 2016/039 ISSN (Print) ISSN (Online) ISBN (Print) ISBN (PDF)

4 This report has been peer reviewed by the Peer Review Panel. Submitted for review on 1 August 2016 Review completed on 26 September 2016 Reviewed by one reviewer Approved for Auckland Council publication by: Name: Dr Lucy Baragwanath Position: Manager, Research and Evaluation Unit (RIMU) Name: Dave Allen Position: Principal Analyst Strategy, Natural Environment Strategy Date: 26 September 2016 Recommended citation Hickey, C W., Williamson, R B., Green, M O and Storey, R G (2016). Technical aspects of integrating water quality science in freshwater and coastal environments. Prepared by NIWA and Diffuse Sources for Auckland Council. Auckland Council technical report, TR2016/039 Cover image: Kaipara River, southern Kaipara Harbour by Jay Farnworth 2016 Auckland Council This publication is provided strictly subject to Auckland Council s copyright and other intellectual property rights (if any) in the publication. Users of the publication may only access, reproduce and use the publication, in a secure digital medium or hard copy, for responsible genuine non-commercial purposes relating to personal, public service or educational purposes, provided that the publication is only ever accurately reproduced and proper attribution of its source, publication date and authorship is attached to any use or reproduction. This publication must not be used in any way for any commercial purpose without the prior written consent of Auckland Council. Auckland Council does not give any warranty whatsoever, including without limitation, as to the availability, accuracy, completeness, currency or reliability of the information or data (including third party data) made available via the publication and expressly disclaim (to the maximum extent permitted in law) all liability for any damage or loss resulting from your use of, or reliance on the publication or the information and data provided via the publication. The publication, information, and data contained within it are provided on an "as is" basis.

5 Technical aspects of integrating water quality science in freshwater and coastal environments C W Hickey National Institute of Water and Atmospheric Research (NIWA) R B Williamson Diffuse Sources Ltd M O Green R G Storey National Institute of Water and Atmospheric Research (NIWA) NIWA Project: ARC14204 NIWA Client Report: HAM

6 Executive summary Auckland Council is currently engaged in a number of significant programmes and projects that focus on how Auckland s natural resources are managed. Two of these programmes are in response to changes at a national level, the National Policy Statement: Freshwater Management 2014 (NPS-FM) with implementation through council s Wai Ora Healthy Waterways Programme and Marine Spatial Planning (MSP) as a preliminary means of addressing aspects of the New Zealand Coastal Policy Statement (NZCPS). There is a clear overlap between the two programmes in the area of water quality, not least the natural river to sea connection between the land, fresh water and coastal environments. A key area of overlap occurs around water quality parameters and the setting of objectives and limits. The latter are required in fresh water by the NPS-FM, whereas objectives and limits are not required by the NZCPS in the coastal environment (though the intent is indicated in Policy 7). It is envisioned that determining values, and developing objectives and limits for the coastal environment would be the logical next steps arising from the MSP process. As a first step, in 2012 Auckland Council commissioned a report which provided a preliminary assessment of limits and guidelines available for classifying coastal waters (Williamson et al., 2016). A similar investigation focusing on the freshwater environment was identified as necessary to develop NPS-FM implementation strategies. The information from the two studies could then be used to guide application of scientific knowledge of water quality to an objectives and limits framework, thereby supporting uses and values of Auckland s fresh and coastal water resources in an integrated manner. The purpose of this report is to provide: a technical assessment of the existing guidelines and limits used to classify freshwater for water quality management purposes; an understanding of the technical considerations required to integrate coastal and freshwater science for the purposes of establishing objectives and limits under the National Policy Statement: Freshwater Management 2014 and the New Zealand Coastal Policy Statement. i

7 Table of contents 1 General Introduction Introduction to Water Classification/Limits Based Approach Approaches to water classification Past approaches Current revision of approaches under the National Policy Statement for Freshwater Management (NPS-FM) Auckland s freshwater bodies Values or uses of water in Auckland Combining water body types, values and attributes Auckland Unitary Plan (PAUP) Part 1: Guidelines 3 General Water Quality: Freshwater Temperature Dissolved oxygen Salinity and conductivity ph Water clarity (and colour) Total Suspended Solids Nutrient Enrichment Overview of eutrophication in New Zealand Use/applicability/importance Critique/review of existing and proposed approaches to nutrient enrichment management/guidelines Relevance/suitability for Auckland Recommendations Toxicants in Surface Waters Introduction Ammonia Nitrate Heavy metals copper (Cu), lead (Pb) and zinc (Zn) Organics ii

8 6 Human Health Human health risks in the aquatic environment Use/applicability/importance Critique/review of existing and proposed approaches to microbial contamination management/guidelines Relevance/suitability for Auckland Recommendations Stream Ecological Valuation (SEV) Overview and importance Use/applicability Critique/review of SEV approach for stream water management Relevance/suitability for Auckland Recommendations Macro-invertebrate Community Index (MCI) Overview and importance Use/applicability Critique/review of the MCI approach for assessing ecological health Relevance/suitability for Auckland Recommendations Bacterial Community Index (BCI) Overview and importance Use/applicability Critique/review of BCI Relevance/suitability for Auckland Recommendations Stream Macrophytes Overview and importance Use/applicability Critique/review of existing approaches for macrophytes management/guidelines Relevance/suitability for Auckland Recommendations iii

9 11 LakeSPI Overview and importance Use/applicability Critique/review of LakeSPI approach to lake management Relevance/suitability for Auckland Recommendations Fish IBI Overview and importance Use/applicability Critique/review of Fish IBI approach to managing freshwater ecosystems Relevance/suitability for Auckland Recommendations Alternative indices Lake Trophic Level Index (TLI) Overview and importance Use/applicability Critique/review of TLI approach to lake management/guidelines Relevance/suitability for Auckland Recommendations CCME Water Quality Index Overview and Importance Use/applicability/importance Critique/review of existing WQI approaches Relevance/suitability for Auckland Recommendations Other Indices iv

10 Part 2: Integrating Coastal and Freshwater Science 16 Integrating Estuary and Freshwater Management Introduction Geophysical differences The NPS-FM Analysis of the limits-based management process under the NPS-FM The Master Attribute Conclusions Potential Conflicts Across All Parameters Summary Abbreviations and Glossary Abbreviations Glossary References Appendices Appendix A: Values and parameters included in this review Appendix B: Numeric environmental management guidelines Appendix C: Other indices Appendix D: National Objectives Framework (NOF) Standards (MfE 2014a) v

11 1 General Introduction Auckland Council is currently engaged in a number of significant programmes and projects that focus on how Auckland s natural resources are managed. Two of these programmes are in response to changes at a national level, the National Policy Statement: Freshwater Management 2014 (NPS-FM) with implementation through council s Freshwater Programme Wai Ora (Auckland Council 2013b), and Marine Spatial Planning (MSP) as a preliminary means of addressing aspects of the New Zealand Coastal Policy Statement. There is a clear overlap between the two programmes in the area of water quality, not least the natural river to sea connection between the land, freshwater and coastal environments. Key areas of overlap occur around water quality parameters and the setting of objectives and limits required for freshwater by the NPS-FM. Objectives and limits in the coastal environment are not required by the NZCPS (though the intent is indicated in Policy 7). It is envisioned that following the MSP process to determine values, developing objectives and limits for the coastal environment would be the logical next steps. As a first step, in 2012 Auckland Council commissioned a report which provided a preliminary assessment of limits and guidelines available for classifying coastal waters (Williamson et al., 2016). A similar investigation focusing on the freshwater environment would be of value to further develop NPS-FM implementation strategies. The two studies can then be drawn upon to provide guidance on how available scientific information on water quality could be applied in an integrated manner to an objectives and limits framework to support uses and values of Auckland s fresh and coastal water resources. This study brief included objectives relating to freshwater guidelines and their linkages with managing the coastal environment. An inception workshop with Auckland Council staff confirmed the scope of the brief. The specific objectives were: Part 1 Objectives: 1A: The analysis and documentation of existing guidelines, numeric objectives and limits based approaches available for freshwater (aquifers, lakes and rivers/streams) for water quality parameters. This is to include any identified combined index measures and proxies (see Williamson et al., 2016). 1B: A critique of the approach and robustness of the guidelines and approaches used for each parameter as well as a technical assessment of each parameter s applicability and relevance to the Auckland environment. Technical aspects of integrating water quality science in freshwater and coastal environments 1

12 1C: Identification of any limitations or opportunities each water quality parameter has that might influence the ability to set effective and efficient objectives and limits in the freshwater environment. This includes consideration of scientific or other limiting factors that may make objective and limit setting challenging i.e., cost (to monitor or to set limits etc.), ability to be monitored efficiently, how easily the parameter can be modelled etc. Part 2 Objectives: 2A: Investigation of technical aspects of setting integrated objectives and limits that support uses and values across coastal and freshwater environments. 2B: Identification of any limitations or opportunities each water quality parameter has that might influence the ability to set effective and efficient objectives and limits across both freshwater and coastal environments (as above). 2C: To establish how integrated objectives and limits are set against the competing values of each environment, whether the receiving environments wholly drive the freshwater objectives and limits and how upstream objectives can be combined or summed to meet those of the receiving environment. This work would also need to have particular regard to the timing and implementation of the two programmes, bearing in mind the different levels of detail they each require as outputs. The environmental values and water quality parameters to be specifically addressed in this review were specified in the brief. These are provided in Appendix 1, which lists 13 values and 25 parameters to be considered for river, lake and groundwater environments. These lists form the basis for our guidelines review. We provide an overview of selection of management parameters in relation to environmental values in section This project does not specifically address statistical considerations in relation to water quality monitoring, nor does it include Maori values, goals and related indicators or guidelines. Both these topic areas were considered out of scope for this project, but would need to be considered as part of an integrated programme. We provide reference to relevant documents in sections of this report where it is relevant to that topic. Consideration of values/objectives of coastal environments outside the coastal marine area was also considered out of scope. Technical aspects of integrating water quality science in freshwater and coastal environments 2

13 This report summarises and describes individual parameters under the following general parameter grouping headings: Chapter 3 - General Water Quality Chapter 4 - Nutrient Enrichment Chapter 5 - Toxicity Chapter 6 - Human Health Chapter 7 - Stream Ecological Valuation (SEV) Chapter 8 - Macro-invertebrate Community Index (MCI) Chapter 9 - Bacterial Community Index (BCI) Chapter 10 - Stream Macrophytes Chapter 11 - Recommendations Chapter 12 - Lake SPI Chapter 13 - Fish IBI Chapter 14 - Lake Trophic Level Index (TLI) Chapter 15 - CCME Water Quality Index Individual or groups of similar parameters, e.g., nutrients, are assessed by considering: 1. A brief overview of environmental issues associated with that parameter. 2. How the parameter is applied or what it is used to represent and manage. 3. A critique and review of existing guideline approaches, and any promising emerging alternatives, indices or combinations. This can include other approaches used in NZ and overseas, and new developments arising from Auckland Council activities or the international literature. The latter source is confined to literature of known relevance to Auckland only, because it would have been an enormous task to do justice to the international literature covering water quality guidelines. 4. The relevance and suitability of the parameter to Auckland, including different water management units. 5. Conclusions and recommendations. Other parameters of potential benefit for managing Auckland s freshwater environment, but not included in the project brief, are also briefly listed for completion. Technical aspects of integrating water quality science in freshwater and coastal environments 3

14 2 Introduction to Water Classification/Limits Based Approach 2.1 Approaches to water classification Management of aquatic environments (e.g., a specific water body type) requires: defining the values identified by the community as priorities for specific catchments, and defining the water quality and physical habitat factors, which together affect the suitability of that environment for supporting a particular value. In this section, we provide an overview on how an integrated framework for freshwater management might be applied to protect various environmental uses and values. Basically we consider which environmental parameters (Appendix A) might be managed across different values (Section 2.5) and water body types (Section 2.6). We review the approach to water classification and limits through briefly considering: 1. Past approaches, including Schedule 3 of the RMA and ANZECC Guidelines. 2. Current revision of approaches under the National Policy Statement for Freshwater Management. 3. Auckland s freshwater bodies (water types). 4. Values or uses of water in Auckland. 5. Combining water body types, values and attributes (often called indicators or measures). The rest of the document provides a simple narrative on the various environmental parameters (National Objectives Framework (NOF): attributes ): see Contents for the way this information has been arranged. We also discuss a number of key additional indicators in section 15 which were not recorded in the brief but may be relevant to integrated freshwater management. Technical aspects of integrating water quality science in freshwater and coastal environments 4

15 2.2 Past approaches There are a number of approaches to freshwater management/guidelines and these vary from parameter to parameter. However, there are 2 main approaches common to most physical, chemical and microbial parameters Schedule 3 of the Resource Management Act (RMA) and the ANZECC (2000) Guidelines. An overview of these are given here for efficiency, while parameter-relevant information in each of these approaches is given in parameter chapters Schedule 3 of the RMA: water quality classes The water quality classes in Schedule 3 of the RMA are summarised in Table 2-1. Several publications supported this Schedule, including the ANZECC Guidelines (ANZECC 1992; ANZECC 2000), guidelines for nutrients (MfE 1992) and for colour and clarity (MfE 1994). Table 2-1 Summary and application of freshwater classification to Auckland water bodies. Schedule 3 of the RMA: water quality classes Class AE Water (being water managed for aquatic ecosystem purposes). Class F Water (being water managed for fishery purposes). Class FS Water (being water managed for fish spawning purposes). Class SG Water (being water managed for the gathering or cultivating of shellfish for human consumption). Class CR Water (being water managed for contact recreation purposes). Class WS Water (being water managed for water supply purposes). Class I Water (being water managed for irrigation/stock water purposes). Class IA Water (being water managed for industrial abstraction). Class NS Water (being water managed in its natural state). Class A Water (being water managed for aesthetic purposes). Class C Water (being water managed for cultural purposes). Water bodies In Auckland Hard-bottomed streams, soft bottomed streams, (rural and urban) ephemeral streams, lakes, estuaries, open coast, natural wetlands. Streams for whitebait, koura, kokopu. Native fish spawning in upper catchments. Stream estuaries for whitebait. Mainly estuaries, but there maybe be opportunities for gathering kaeo (freshwater mussels). All Water supply lakes and feeder streams in Hunua, Waitakere. Streams in native bush areas. Groundwater aquifers. Streams in rural areas or draining to rural areas. Groundwater aquifers. Streams in developed land use or draining to developed areas. Groundwater aquifers. Potentially headwater streams in native bush areas. Unknown Unknown Technical aspects of integrating water quality science in freshwater and coastal environments 5

16 2.2.2 ANZECC (2000) guidelines These publications offered guidelines for the comprehensive management of water bodies in Australia and New Zealand. The primary (first and foremost) principle in the ANZECC guidelines is to decide how specific sites are to be managed by defining primary management aims. This leads to the guideline procedures for classifying ecosystems as pristine and undisturbed (Condition 1), slightly to moderately disturbed (Condition 2) and highly disturbed (Condition 3). For condition 2 and 3, the guidelines ensure that these are adequately protected by identifying and specifying the levels of protection for these conditions (e.g., 80%, 95%, 99%). For ecosystems requiring the highest protection, Condition 1, the objective of water quality management is to ensure that there is no detectable change (beyond natural variability) in the levels of stressors. The guideline values in ANZECC are termed trigger values, implying that additional consideration may be required if these values are exceeded. For example, this might include assessing dissolved metal concentrations or providing a water hardness adjustment prior to comparison with the trigger value. For physical and chemical stressors in ANZECC (2000), trigger values for key performance indicators have been determined by comparison with suitable reference ecosystems. This is in contrast with other guidelines, which are based on cause/effect (e.g., toxicity). We point out that the uncritical use of the numerical physico-chemical trigger values that are listed in the ANZECC guidelines contradicts the ANZECC guidelines approach. Some numerical values are not appropriate to Auckland, and, consistent with the ANZECC Guideline approach, local numerical values have to be derived for some parameters using a reference site (condition) approach. We address this further in the following section. An approach to guidelines promulgated by ANZECC (2000) is to define physicochemical trigger values below which there is a low risk of any adverse effects. Ideally thresholds for trigger values would be developed from actual studies of ecological effects, however, in the absence of such information, the 80 th (or 20 th ) percentile for slightly to moderately disturbed ecosystems is suggested as a guide. Appendix B (Table B2) lists the 80 th percentiles (or 20 th percentiles) as summarised by ANZECC (2000) for New Zealand waters. The statistical data were from the lowland rivers (three rivers) and upland rivers (18 rivers) from the National River Water Quality Network (NRWQN) (Davies-Colley 2000). It is evident that many of these water quality parameters will not indicate anything useful about the thresholds or tolerance levels for aquatic ecosystems. In particular, the trigger values for ammoniacal-n, dissolved oxygen and ph are not likely to be helpful, being well within the guideline values for protection from adverse biological effects. For example, the ANZECC (2000) physico-chemical trigger values for ammoniacal-n Technical aspects of integrating water quality science in freshwater and coastal environments 6

17 provide values of 10 µg NH 4 -N/L in upland and 21 µg NH 4 -N/L in lowland rivers (Table B2). These values do not represent any basis for the establishment of adverse ecosystem effects. As such, they should not be used in a regulatory context. However, the percentiles in Table B2 may provide some useful benchmark values for some purposes, in the absence of suitable water quality data being available for local reference sites. The general approach used in the ANZECC (2000) guidelines to derive physicochemical water quality benchmark concentrations would be applicable to the derivation of Auckland region-specific data and potential triggers for management bands. However, the methods used to develop management bands for lower protection levels require the analysis of environmental gradients in order to establish thresholds linked to ecological or other effects (e.g., aesthetic, recreational, mahinga kai). This work has not been undertaken for Auckland streams or rivers Summary of present guidelines The currently available narrative or numeric guidelines or standards for the specified environmental parameters (Appendix A), and their relevance to rivers, lakes or groundwater environments is summarised in Table 2-2. These guidelines and standards are summarised from a number of sources, principally RMA (1991), Ministry of Health (MOH 2008) NOF (MfE 2014a) and ANZECC (2000). We have included mahinga kai under Aquaculture as we consider that this would represent a minimum suite of relevant parameters in the absence of an expanded suite which might be applicable to mahinga kai (e.g., inclusion of habitat and aesthetic values). The numeric values and various protection levels currently available under the NOF process (MfE 2014a) are provided in Appendix B, together with proposed numeric values for ph and temperature (Davies-Colley et al. 2013). A number of the environmental monitoring parameters proposed for freshwater bodies in Auckland are incorporated into, or proposed for, the water state-ofenvironment (SoE) reporting in New Zealand. A review of the relevance and monitoring costs of SoE variables was undertaken as part of the standardisation of quality assurance aspects of the National Environmental Monitoring and Reporting (NEMaR) project (Davies-Colley et al. 2012a). The assessments included in that report will complement the information provided in this report on the environmental monitoring parameters for freshwater bodies in Auckland. Technical aspects of integrating water quality science in freshwater and coastal environments 7

18 Table 2-2 Currently available guidelines and standards for different values in various water body types (R = river, L = lake, G = groundwater; (t) = post treatment removal; na = not applicable). Ecosystem health Human health: Drinking water Human health: Consumption Human: Recreation (primary contact) (ANZECC) Human: Recreation (secondary contact) Aesthetic Stock water Irrigation Parameter Components Temperature R R,L ph R R,L,G R,L R,L Dissolved oxygen R,L,G R,L R,L Clarity R,L R,L Turbidity R,L R,L,G (t) R,L R,L Total suspended solids R,L R,L Salinity (chloride) R,L R,L,G (t) R,L R,L,G Conductivity (total dissolved solids) R,L R,L Total nitrogen L R,L,G Total phosphorus L R,L,G R,L Nitrate nitrogen (toxicity) R,L R,L,G R,L R,L,G R,L Nitrate nitrogen (eutrophication) R,L Nitrite nitrogen (toxicity) R,L R,L,G R,L R,L,G R,L Hardness R,L,G (t) R,L R,L Ammoniacal nitrogen R,L R,L,G (t) R,L R,L Dissolved reactive phosphorus R Chlorophyll a R,L Macrophytes R,L R,L Periphyton R R,L Colour R,L,G (t) R,L Oil & Grease R,L R,L Microbiological E.coli R,L,G R,L,G R,L,G R,L R,L R,L,G R,L,G Enterococci R,L,G Campylobacter R,L,G Viruses R,L,G Cyanobacteria (planktonic) R,L,G R,L R,L R,L,G Cyanobacteria (benthic) R Cyanobacteria (microcystins) R,L,G R,L,G R,L R,L R,L,G Metals Copper R,L,G R,L,G (t) R,L R,L,G R,L,G R,L Zinc R,L,G R,L,G (t) R,L R,L,G R,L,G R,L Lead R,L,G R,L,G (t) R,L R,L,G R,L,G R,L Cadmium R,L,G R,L,G (t) R,L,G R,L R,L,G R,L,G R,L Iron R,L,G R,L,G (t) R,L R R,L,G R,L Manganese R,L,G R,L,G (t) R,L R,L,G R,L Aluminium R,L,G R,L,G (t) R,L R,L,G R,L,G R,L Metaloids Arsenic R,L,G R,L,G (t) R,L,G R,L R,L,G R,L,G R,L Non-metalic inorganics Boron R,L,G R,L,G R,L R,L,G R,L,G Fluoride R,L,G R,L,G R,L,G R,L,G R,L Hydrogen sulphide R,L,G R,L,G (t) R,L Macroinvertebrate community index (MCI) R Fish IBI R OIBI R River connectivity R Lake SPI L Habitat R,L Stream Ecological Valuation (SEV) R Rotifer index L CCME water quality index Various na na Aquaculture (Mahinga kai) Technical aspects of integrating water quality science in freshwater and coastal environments 8

19 2.3 Current revision of approaches under the National Policy Statement for Freshwater Management (NPS-FM) Introduction Until recently, NZ waters were largely managed from an effects-based approach under the RMA, based largely on the application of water quality guidelines. There were few national standards to be considered for inclusion into regional rules and planning documents. The National Policy Statement for Freshwater Management (NPS- FM) establishes a legal and policy framework for building a national limits-based approach to freshwater management. The NPS-FM is introduced under the RMA, it does not replace the RMA. water/freshwater-reform-2013 The NPS-FM requires: overall water quality in a region to be maintained or improved safe-guarding the life-supporting capacity, ecosystem processes and indigenous species (including their associated ecosystems) of fresh water, and safe-guarding the health of people and communities, at least as affected by secondary contact with freshwater. Councils are required to, by 2025, to have Set freshwater objectives that reflect national and local values. Set flow, allocation and water quality limits to ensure freshwater objectives are achieved. Addressed over-allocation. Established processes that allow land use and water to be managed in an integrated way. Involved iwi and hapū in freshwater decision-making. Councils and communities can choose the timeframes to meet freshwater objectives and limits. Technical aspects of integrating water quality science in freshwater and coastal environments 9

20 The NPS-FM is currently at various stages of implementation around the country as regional councils give effect to their policies through regional plans. Freshwater objectives describe the intended environmental outcome(s) (definition from National Policy Statement for Freshwater Management). Freshwater objectives are set in regional planning documents and describe the desired state of the water body, having taken into account all desired values. Values (equivalent to uses) can include any national value, and any value in relation to fresh water which a regional council identifies as appropriate for regional or local circumstances. The NPS-FM uses limits, attributes and targets to meet freshwater objectives. Limits refer to maximum resource limits available, that allows a freshwater objective to be met. Limits can be expressed as m 3 /sec, m 3 /yr or tonnes/yr (for example). Attributes are measurable characteristic of fresh water, including physical, chemical and biological properties, which supports particular values. A range in the level of an attribute that may be described as a narrative or numerically. Four different numerical states are specified for attributes (A, B, C or D). Targets can be specified to be met in the future within a specific timeframe. Implementation of targets can take into account investment, good management practice (also called BMP), regional programmes, incentives, regulation (e.g., for land use). Targets can be specified in many ways, e.g., tonne N/yr Links between NPS-FM values, objectives, limits and management actions The following diagram (Figure 2-1) illustrates the link between objectives, limits and methods. Figure 2-2 provides an illustration of this management process using nitrate toxicity as an example. Figure 2-1 Generalised diagram of the links between values, objectives, limits and management actions 1. 1 Adapted from Environment Canterbury Technical Report for Hurunui Catchment, 2010 (MfE 2015). Technical aspects of integrating water quality science in freshwater and coastal environments 10

21 Figure 2-2 Diagram of the links between values, objectives, limits and management actions specific to the nitrate toxicity attribute (MfE 2015). This illustrates the process undertaken in the NOF whereby narrative and numeric objectives are related to final catchment management actions in terms of load limits. For some parameters, such as nutrients in rivers, a measure such as filamentous periphyton cover is used rather than specific nutrient concentration objectives National Objectives Framework attributes The National Objectives Framework (NOF) provides an approach to establish freshwater objectives for national or regional values. The approach uses numerical or narrative attributes to achieve this. The attributes shown in Table 2-3 are those envisaged as part of the NOF programme as at 2013 (grey boxes) (MfE 2013). It also indicates the attributes that may be included in future amendments once the science is agreed (white boxes with a tick). Temperature and ph are not in the current NOF standards but thresholds have been proposed for these parameters (Davies-Colley et al. 2013). The MfE draft implementation guide (MfE 2014b) states that: Other attributes that are not yet in Appendix 2 [of the NPS-FM] may also be required (such as sediment, temperature and clarity). Work is continuing to further populate the attributes of Appendix 2, but in the meantime regional councils will need to develop freshwater objectives for other attributes in their freshwater management units (FMUs) that are applicable to the value and water body type. (p2). The two compulsory values (Ecosystem health and Human health secondary contact) are shown, and mahinga kai is included below as an example of an attribute that will be added in the future for this value. This table illustrates that a suite of attributes (also more generally termed parameters) are required to manage values, such as ecosystem health, and identifies the limited number of attributes that have been included in the gazetted Technical aspects of integrating water quality science in freshwater and coastal environments 11

22 standards (grey shaded 2 ) (MfE 2014a). These standards provide numeric and narrative attribute states for the National Bottom Line and three attribute states for a range of water quality parameters. This is consistent with the approach used in ANZECC (2000) for different levels of protection/different levels of disturbance. Some attributes, such as temperature and ph for streams and rivers have had proposed states developed for the NOF thresholds (Davies-Colley et al. 2013). Future planned reviews of the NOF will incorporate additional parameters in the suite of standards for application to rivers and lakes. Draft guidance for the implementation of NOF standards has been produced (MfE 2014b), but technical guidance has yet to be produced as of December A major component of the implementation guidance will relate to the Freshwater Management Unit (FMU) which is the spatially distinct unit where defined water management policies will apply (as published in June 2016). Monitoring and statistical guidance will also be required to support the comparison of field-collected data with the various standards. 2 As proposed except for nitrate toxicity in lakes where the total nitrogen guidelines were considered suitable low to preclude the possibility of nitrate toxicity. Technical aspects of integrating water quality science in freshwater and coastal environments 12

23 Table 2-3 Proposed National Objectives Framework (NOF) attributes for freshwater environments as at 2013 (from MfE 2013). Technical aspects of integrating water quality science in freshwater and coastal environments 13

24 2.4 Auckland s freshwater bodies The NPS-FM requires that regional councils identify all freshwater management units in their region. The nature of Auckland s freshwater bodies has been described in a recent report (Phillips et al. 2013). The rest of this section was adapted from that report and is reproduced for convenience here. The Auckland Council Regional Plan: Air, Land and Water (Auckland Council 2013a) defines and manages rivers and streams as one of two types, depending on the permanence of their hydrology or year-round existence. The Proposed Auckland Unitary Plan (PAUP) (Auckland Council 2016) defines river or stream as including permanent or intermittent reaches, but excludes ephemeral reaches (Part 3 Regional and District Rules Chapter H; Auckland-wide rules, Section 4 Natural Resources 4.13 Lakes, Rivers, Streams and Wetland Management). This PAUP also identifies management areas based on stream type, wetlands and lake type. The Auckland region has around 16,500 km of permanent rivers. No mainland location in the Auckland region is more than 20 km from the coast, thus the catchment areas of each river are relatively small. This means that most of the rivers reach the sea before they merge with others to form large rivers. The majority (approximately 90%) of streams in the Auckland Region are short (first or second order), narrow (channel width <2 metres), and contained within small (<100 ha) catchments (ARC 2004a). Only 3 per cent of the rivers are fifth order and greater. Urban streams are categorised according to level of disturbance, and include river mouths and tidal reaches. River water quality is strongly related to the type of land cover in the surrounding catchment area. Native forest sites have the best water quality and urban sites have the worst. The relatively low elevation of the Auckland region and the underlying geology of the land also have a profound influence on the nature of the rivers, usually resulting in slow flowing, low gradient rivers with soft-bottomed beds. Fast flowing, high gradient rivers with stony, hard bottoms are mostly restricted to catchments that drain the higher areas in the Waitakere Ranges, the Hunua Ranges, and the offshore islands (e.g., Great Barrier Island). The Auckland region has 72 lakes, most of which are small in a national context. Most of these are dune lakes formed by the impoundment of water behind sand dunes blown in from coastal beaches. Both rural and urban lakes are classified. Although the water quality of monitored lakes is generally classified as degraded, due principally to nutrient enrichment, microbiological lake water quality is usually good when compared with national guidelines for recreation. There is no clear trend in lake water quality (water quality in some lakes had improved, some had got worse Technical aspects of integrating water quality science in freshwater and coastal environments 14

25 and some had not changed). The ecology of the lakes was impaired, with exotic species (plants and/or fish) considered to be the main cause of environmental stress. Important groundwater resources are classed as quality sensitive aquifers. The Auckland region has a number of significant aquifers in both rural and urban areas, which are important as direct sources of water supply for domestic and commercial use. They are also major contributors to the base flow of many streams, particularly in the southern parts of the region. Known geothermal groundwaters are located at Parakai, Waiwera, Whitford and Great Barrier Island. Wetlands include permanently and intermittently wet areas, shallow water and land/water margins that support a natural ecosystem of plants and animals that are adapted to wet conditions. Generally these include areas of marsh, fern, peat land or brackish water. 2.5 Values or uses of water in Auckland As discussed previously, the NPS-FM requires regional councils to identify freshwater management values relevant to the local context. The potential values to be used in Auckland's freshwater management are listed below. These values were based on a recommended suite of values for Auckland freshwaters, including specific values in three major categories: ecosystems ; use and social, and cultural (ASL 2013). The ASL report excluded the following values: trout fishing; boating and navigation; freshwater aquaculture; electricity generation and ceremonial uses. The values water abstraction and stormwater conveyance were included in the ASL recommendations but were excluded from the brief for this project. The suite of values includes those proposed by the NPS-FM, including the two compulsory values of Ecosystem health and Human health secondary contact recreation (MfE 2013). 1. Natural State 2. Ecosystem Health 3. Domestic Use 4. Industrial Use 5. Public Water Supply 6. Stock Watering 7. Irrigation 8. Food production and harvest 9. Primary Contact 10. Secondary Contact 11. Aesthetics/Visual amenity Technical aspects of integrating water quality science in freshwater and coastal environments 15

26 12. Tangata whenua values Te Mana o te Wai (mahinga kai, mauri, wai tapu) 13. Fisheries (Fish spawning other). 2.6 Combining water body types, values and attributes The matrix for management of various values requires reconciling both: multiple parameters for a particular value (e.g., Ecosystem health) (Table 2-3), and multiple guidelines or standards (Table 2-4) relating to more than one use or value in a given catchment. While this exercise is relatively straight forward for point source discharges, where the environmental changes may be limited to water quality parameters, the management issues become much more complex for the management of diffuse contaminants and associated land-use activity. The relative importance of the environmental parameters (attributes) varies, sometimes greatly, across water body and value. This is illustrated in Table 2-3. In this illustrative example we have expanded the Ecosystem health value to address parameters relevant to hard-bottom streams, soft-bottom streams, lakes and wetlands. The basis for this distinction is that measures associated with the monitoring parameters have been associated with different ecological measures in specific aquatic environments (e.g., macroinvertebrate indices for soft-bottom streams (Maxted et al. 2003; Stark et al. 2007b); macrophytes in lakes (de Winton et al. 2012) or rivers (Matheson et al. 2012)), or required reference sites in the appropriate environments (e.g., the Stream Ecological Evaluation (SEV) (Storey et al. 2011)). This distinction is particularly relevant to habitat-related factors factors affecting the suitability of the habitat for specific ecological communities. Further environmental classification may be useful for management values associated with some habitats, such as urban streams where a range of classifications are recognised which will reflect the susceptibility to various multiple stressors (ARC 2004a). Table 2-4 lists some of the other values from Section 2.5, and shows the relative importance of the parameters for different uses. For simplicity and greater transparency, Table 2-4 combines and separates some values. Primary and secondary recreation have been combined under human health. Domestic use is included in potable water supply. Food production and harvesting has been split into aquaculture and human consumption (of freshwater resources), which also includes mahinga kai. Technical aspects of integrating water quality science in freshwater and coastal environments 16

27 Table 2-4 Qualitative assessment of the effects of water quality parameters on major values associated with freshwater ecosystem uses. Values Aquaculture or harvesting Human Health- Recreation Human health consumption Irrigation & stock water Industrial abstraction Cultural Natural Aesthetics Parameters HB streams SB streams Urban streams Lakes Wetlands Temperature ph Dissolved oxygen Clarity Turbidity Salinity Sediment/Suspended Solids TN, TP, trophic status Nitrate toxicity Ammonia Toxicity (Ammoniacal Nitrogen) Nutrients e.g., N, P, ammonia, chlorophyll a Periphyton (rivers) Microbiological e.g., E.coli Cyanobacteria Heavy metals e.g., copper, zinc, lead, cadmium in water and in sediments Conductivity Habitat MCI (SBMCI) Fish Productivity River Connectivity Stream Ecological Valuation (SEV) Lake SPI / River macrophytes Rotifer Index QIBI N/a Fish IBI CCME Water Quality Index ARC index N/a HB streams All others All All All Surface water Groundwater All All Ecological integrity Fisheries All Potable Water supply All All KEY Highly useful and relevant 1 Moderately useful or relevant 2 Unlikley to be useful, poor relationship 3 May be useful in interpretation or may affect other parameters that are directly relevant Not useful or relevant 4 Notes: Urban streams have a range of classifications which will reflect ecological values and the potential suceptability to stressors. Six type categories are recognised by Auckland Council, ranging from high value low disturbance to piped channels (ARC 2004a). Abbreviations: HB and SB streams = hard-bottom and soft-bottom streams A process of reconciliation needs to be undertaken for multiple guidelines and standards which are applicable to the freshwater uses and values. Figure 2-3 illustrates this process for water quality objectives from the ANZECC (2000) guidance. The process involves: (i) determining the various use-related guidelines to establish the limiting value; (ii) comparison with existing water quality; and (iii) consideration of societal aspirations. This process is similar to that proposed for the implementation of multiple NOF numeric standards, although specific guidance covering the water management units and frequency of monitoring has not yet been provided. The Economic and Social factors component in Figure 2-3 is the community consultation process that identifies the relevant band for a particular Technical aspects of integrating water quality science in freshwater and coastal environments 17

28 value. This process may translate to a lower level of protection (i.e., a different NOF band, equivalent to different ANZECC protection levels for chemical contaminants) for some values. The final numeric water quality objective (WQO) for a water body will be the lowest value from the range of attributes and bands required to support the uses (i.e., values) in that water body. Extending this process to a larger number of parameters requires consideration of more guidelines and standards. Our qualitative assessment framework illustrates how this process could be implemented for various values whereby high relevance parameters (green 1 in Table 2-4) would be the key parameters required for management of that value. It is worth noting that a number of parameters are not relevant to specific uses and therefore do not require consideration. Figure 2-3 Schematic showing consideration of multiple freshwater guidelines for establishing water quality objectives (based on ANZECC 2000 guidance). Water quality indicators are equivalent to the term parameters/attributes as used in this report. 2.7 Auckland Unitary Plan (PAUP) Auckland Council released the Proposed Auckland Unitary Plan (PAUP) Decision Version in August 2016 (Auckland Council 2016). The PAUP includes objectives and policies for water quality and integrated management. It provides an overall framework for managing the individual and cumulative adverse effects of activities that affect freshwater systems and coastal waters, by the use of a surface water quality interim guideline and a range of discharge and activity based land use management controls. Technical aspects of integrating water quality science in freshwater and coastal environments 18

29 The interim freshwater quality guideline uses the presence and sensitivity of macroinvertebrates in streams in different land use catchments as a surrogate for multifactor water quality standards. Experience suggests that if macroinvertebrate health is maintained, other factors including food gathering and recreational values of freshwater are also maintained. This interim guideline will be replaced over the next ten years by more comprehensive water quality and quantity objectives and limits to be developed in accordance with the NPS-FM and subsequently given effect to through the PAUP (section E1 Water Quality and Integrated Management). The specific policies for surface water quality and ecosystem health interim guidelines are: 1. Manage the cumulative effects of land use and development and control the discharge of water and contaminants to land and freshwater systems by using the Macroinvertebrate Community Index (MCI) as a measure of freshwater ecosystem health associated with different land uses within catchments. 2. Manage discharges, land use and development and activities that may affect freshwater systems to, as far as practicable: a. maintain water quality, flows, stream channels and their margins and other freshwater values, where the MCI currently meets or exceeds the relevant guideline 3 : MCI guideline for Auckland rivers and streams b. restore or enhance water quality, flows, stream channels and their margins and other freshwater values where the MCI guideline in Table 1: MCI guideline for Auckland rivers and streams are not currently met c. retain, and where practicable enhance, existing freshwater values where there is a change to an urban land use. 3. Require freshwater values to be enhanced unless existing intensive land use and development and irreversible modification of stream channels practicably precludes enhancement occurring. 4. Develop catchment specific objectives and limits for freshwater with Mana Whenua through community consultation, scientific research and mātauranga Māori, to replace the MCI guideline and to give effect to the NPS-FM. 3 The proposed MCI guidelines for Auckland rivers and streams are: native forest, 123; exotic forest, 111; rural areas, 94; and urban areas, 68 (section E1, Table E1.3.1). Technical aspects of integrating water quality science in freshwater and coastal environments 19

30 3 General Water Quality: Freshwater This section covers the range of parameters specified for detailed assessment (Appendix 1). Additional parameters which may be relevant for freshwater ecosystem management purposes are addressed in section Temperature A large part of the following is summarised from Davies Colley et al. (2013). This report includes information from a review of thermal tolerance for native aquatic biota (Olsen et al. 2012) Overview/Issues Temperature affects aquatic ecosystems because it affects oxygen solubility and other chemical constituents (e.g., ammonia toxicity), but more particularly because it affects the growth of most aquatic organisms. The temperature of maximum growth rate is referred to as the temperature optimum. Temperatures above the growth optimum impose thermal stress on organisms, and lethal effects are reached only slightly higher than (perhaps 5 C above) the growth optimum temperature. On a seasonal basis, fastest heating, and therefore fastest rate of temperature rise, occurs near the summer solstice (22 December). Maximum temperatures are typically achieved a little later, in late January to early February. Stream and river temperatures also vary diurnally, with temperature reaching a maximum in the mid to late afternoon with fairly rapid cooling through the remainder of the day so that minimum water temperatures occur near dawn. The thermal effects of stormwater runoff are a significant management issue in urban environments. Stream inflows from hard surfaces and treatment devices, such as retention ponds, may result in rapid increases in downstream temperature during rainfall events and prolonged thermal elevation of baseflows. Rural streams may experience marked hydrological alterations which affect thermal regimes, including: abstractions which reduce flow; groundwater inflows; small ponds resulting in marked increases in downstream temperature during summer periods (Maxted et al. 2005): and large dams and reservoirs which commonly result in marked downstream changes in the thermal regime (Gibbs et al. 2012). The nature of riparian shade markedly affects the level of direct solar radiation and the microclimate in the riparian vegetation adjacent to rural streams (Collier et al. 1995; Davies-Colley et al. 2000). Technical aspects of integrating water quality science in freshwater and coastal environments 20

31 3.1.2 Use/applicability/importance Temperature is a key water quality characteristic affecting the health of native fish, macroinvertebrates, and exotic sports fish (e.g., trout). It also strongly influences water composition (for instance, the solubility of dissolved oxygen, the speciation of ammonia). It also affects rates of physico-chemical and biochemical reactions (notably the rate of dissolved oxygen consumption by bacterial respiration) Critique/review of existing and proposed approaches to temperature management/guidelines Existing numerical guidelines are summarised in Appendix Table B2. Schedule 3 RMA Schedule 3 specifies temperature conditions for Class AE, F, FS, and SG waters. Temperature criteria are implicit in Class NS and C waters (Table 3-1). Table 3-1 Standards for Water Quality Classes for Temperature from Schedule 3 RMA. Class Purpose Criteria AE Aquatic ecosystem The natural temperature of the water shall not be changed more than 3 C F Fisheries The natural temperature of the water (a) shall not be changed more than 3 C (b) shall not exceed 25 C. FS Fish spawning The natural temperature of the water shall not be changed more than 3 C. The temperature of the water shall not adversely affect the spawning of the specified fish species during the spawning season SG Gathering or cultivating of shellfish The natural temperature of the water shall not be changed more than 3 C WS Water supply - I Irrigation - CR Contact recreation - IA Industrial abstraction - NS Natural state The natural quality of the water shall not be altered A Aesthetic - C Cultural purposes The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values ANZECC Guidelines ANZECC (2000) specifies that the maximum permissible increase in the natural temperature of any inland waters should not exceed the 80 th percentile of the Technical aspects of integrating water quality science in freshwater and coastal environments 21

32 temperatures measured in reference ecosystems, or a maximum permissible temperature for long-term exposure calculated from the temperature for optimum growth and the incipient lethal temperature, whichever is the least. The maximum permissible temperature for long-term exposure is calculated from an equation given in the USEPA Quality Criteria for Water - Gold Book (US EPA 1986). The ANZECC (2000) guidelines also provide trigger values for physical and chemical stressors based on statistical analysis of regional monitoring data from reference sites in Australia and New Zealand (ANZECC, 2000; section ). The default trigger values in the ANZECC guidelines were derived from ecosystem data for unmodified or slightly-modified ecosystems supplied by state agencies. The choice of these reference systems was not based on any objective biological criteria. As such, the physical and chemical trigger values do not represent thresholds for adverse effects on the respective ecosystems. Auckland Council Water Quality Index (WQI) Temperature is currently measured monthly at 34 river and stream sites for State of the Environment (SoE) monitoring, with a requirement of <18 C for this parameter as one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). Review of Auckland urban stormwater and streams A review of effects of stormwater runoff and temperature regimes in Auckland stream catchments has recommended a maximum daily average temperature criterion of 20 C for management of all Auckland streams for the protection of ecology (Young et al. 2013). The guidance provided in that review is related to stormwater discharge management and does not relate to NOF bands (see next) or to classification of urban stream reach types (ARC 2004a). NPS-FM The NOF has specified that temperature is used as an attribute to protect freshwater values. As of July 2016, there are no nationally-available attribute bands. The Ministry for the Environment requested that NIWA outline a NOF for rivers to protect the value Ecosystem Health for the attributes: temperature, dissolved oxygen and ph. Davies-Colley et al. (2013) reviewed approaches overseas as well as New Zealand data to generate specific NOF bands (A, B, C, D) for temperature (Table 3-2). The review was substantially based on a critical review Water temperature criteria for native aquatic biota prepared for Auckland Council (Olsen et al. 2012). Davies-Colley et al. specified the temperature thresholds using the Cox-Rutherford Index (CRI). This is defined as the average of the mean daily and daily maximum temperatures, and is proposed because it permits direct application of constant Technical aspects of integrating water quality science in freshwater and coastal environments 22

33 temperature criteria from laboratory experiments. They proposed that if the CRI averaged over the five hottest days in summer exceeded relevant thresholds, this would indicate exposure of resident organisms to thermal regimes consistent with the narrative thresholds. They point out that it is most likely thermally stressful conditions will occur during a period of long, clear, dry summer days, and therefore high CRI values will occur in a series of consecutive days. Their summer period has been defined as 1 December to 31 March to encompass the maximum temperatures typically occurring in New Zealand streams and rivers. To account for regionality of temperature, a better way in principle is to refer stressful mid-summer conditions to near-pristine reference streams. Accordingly, in addition to absolute temperature limits they also proposed relative temperature limits as increments for stressful high temperatures above those modelled or measured in nearby reference streams (Table 3.2). Table 3-2 Proposed NOF for temperature regime in rivers and streams (and groundwater, lakes and estuaries) in Maritime regions of New Zealand. The term temperature regime is a reminder that account must be taken of the diel fluctuation of temperature around the daily mean especially in summer when animals are most likely to be exposed each day for a few hours in the afternoons to particularly high temperatures. (Davies-Colley et al. 2013). NOF Band Band descriptors (narrative what Absolute Increment of CRI will people notice as the impact on the value) values of CRI compared to reference site a A No thermal stress on any aquatic organisms that are present at matched 18 C 1 C reference (near-pristine) sites. B Minor thermal stress on occasion (clear days in summer) on particularly 20 C 2 C sensitive organisms such as certain insects and fish. C Some thermal stress on occasion, with elimination of certain sensitive insects 24 C 3 C and absence of certain sensitive fish. D (unacceptable Significant thermal stress on a range of aquatic organisms. Risk of local >24 C >3 C /does not elimination of keystone species with provide for loss of ecological integrity. value) a CRI = Cox-Rutherford index Technical aspects of integrating water quality science in freshwater and coastal environments 23

34 In aquatic ecosystems, temperature, dissolved oxygen (DO) and ph are closely interrelated. Therefore Davies-Colley et al. (2013) describe how the attributes temperature, DO and ph may interact, and how to conduct continuous monitoring so that limits for these variables can be applied. The proposed NOF bands for Maritime Regions are a substantial departure from the standards promulgated under the RMA. Under the RMA, in some situations, the allowable temperature changes would have been equivalent to the C Band - Some thermal stress on occasion, with elimination of certain sensitive insects and absence of certain sensitive fish. The recommended a maximum daily average temperature criterion of 20 C for management of all Auckland streams for the protection of ecology (Young et al. 2013) approximately equates to the B band in the proposed NOF bands Relevance/suitability for Auckland In Auckland, as in other parts of New Zealand, high temperatures are probably commonly encountered during summer, in unshaded, slow-flowing, lowland streams and in urban streams during storm runoff from large impervious surfaces or treatment ponds/wetlands. The proposed NOF bands for temperature regime in rivers and streams (and groundwater, lakes and estuaries) in Maritime regions of New Zealand are highly relevant to Auckland because they were substantially based on a critical review Water temperature criteria for native aquatic biota prepared for Auckland Council (Olsen et al. 2012). These will probably supplant Schedule 3 numerical values. They will probably be appropriate for larger rural streams and rivers, but their relevance to stream ecology may have to be assessed for small lowland rural streams and urban streams. The Young et al. (2013) study is obviously relevant to Auckland Conclusions/Recommendations Recommendations for temperature guidelines are premature until MfE have finalised temperature attributes in the NOF. However, even when these are available, their applicability to all Freshwater Management Units, especially small lowland streams, would need to be critically assessed for the Auckland region. Critical comparisons between NOF bands and recommended maximum temperatures for urban streams (Young et al. 2013) will need to be undertaken. Monitoring requirements, such as those proposed by Davies-Colley et al. (2013), will also need to be assessed, including measuring actual temperature upper limits (rather than changes), continuous monitoring, and the requirement to consider impacts on DO and ph when considering temperature. Continuous monitoring is fairly straight-forward for temperature because simple inexpensive temperature Technical aspects of integrating water quality science in freshwater and coastal environments 24

35 probes are available. Procedures for processing and assessing temperature data will need to be developed and put in place to expedite temperature reporting (Davies- Colley et al. 2012a). In the meantime, there is existing guidance. For stormwater runoff, an interim maximum daily average temperature criterion of 20⁰C could be adopted to the protection the ecology of Auckland urban streams (Young et al. 2013). Guidance related to rural streams awaits further work by MfE to develop attributes for the NPS- FM, such as those proposed by Davies-Colley et al. (2013). Any monitoring should be carried out during summer and at critical times of day preferably continuous monitoring. The proposed NOF bands would be appropriate for the values: aquatic ecosystem, fisheries, fish spawning, aquaculture, mahinga kai and natural waters. 3.2 Dissolved oxygen Overview/Issues Maintaining adequate dissolved oxygen (DO) concentrations is key to achieving healthy aquatic systems - guidelines maintain DO at sufficiently high concentrations to prevent adverse effects on freshwater organisms. Reduced DO levels (hypoxia) can impair the growth and/or reproduction of aquatic organisms and very low or zero dissolved oxygen levels (anoxia) will kill organisms. Water bodies can experience lower DO due to discharge of substances that deplete oxygen during microbial respiration. These substances have elevated Biochemical Oxygen Demand (BOD). These materials may also arise through die-off of algal blooms. Unacceptably low DO concentrations would be managed by controlling discharges and eutrophication. Elevated BOD in waters entering groundwater can also lead to low DO in groundwater. In addition to the causes of low DO conditions mentioned above, lakes (and estuaries) may also experience lower DO due to benthic sediment oxygen demand (SOD). DO depletion in these water bodies can be exacerbated by sheltered conditions (and hence reduced wind mixing and re-aeration), and poor mixing (e.g., caused by density gradient/salt wedges). Significant super-saturation of DO concentrations may occur when excessive algae or macrophyte biomass is present. No adverse ecological effects will occur from high DO concentrations caused by photosynthesis though these often occur in systems with elevated temperature, which will affect biological communities. Adverse effects of total gas pressure (i.e., DO and nitrogen) are related to overpressure below hydroelectric operations and downstream of pumps. Technical aspects of integrating water quality science in freshwater and coastal environments 25

36 These and other processes are well understood. The other main controls of DO are: Re-aeration: the transfer of atmospheric oxygen to water. Photosynthesis: plants and algae release oxygen into the water during photosynthesis. Respiration: plants and algae consume oxygen from the water during respiration Use/applicability/importance DO is a key water quality parameter for measuring the life supporting capacity and its concentration can be affected by many processes, some of which are greatly altered by human development of the environment (such as removal of shade, nutrient enrichment of waterways, discharges of ammonia and biodegradable organic matter) Critique/review of existing and proposed approaches to temperature management/guidelines A summary of existing numerical guidelines is available in Appendix Table B2. DO criteria used throughout the world are reasonably soundly based and widely accepted, including in New Zealand. Schedule 3 RMA Schedule 3 specifies DO conditions for Class AE, F, FS, and SG as The concentration of dissolved oxygen shall exceed 80% of saturation concentration. DO criteria are implicit in Class IA, NS and C (Table 3-3). Technical aspects of integrating water quality science in freshwater and coastal environments 26

37 Table 3-3 Standards for Water Quality Classes for Dissolved Oxygen from Schedule 3 RMA. Class Purpose Criteria AE Aquatic ecosystem The concentration of dissolved oxygen shall exceed 80% of saturation concentration F Fisheries The concentration of dissolved oxygen shall exceed 80% of saturation concentration FS Fish spawning The concentration of dissolved oxygen shall exceed 80% of saturation concentration SG Gathering or cultivating of shellfish The concentration of dissolved oxygen shall exceed 80% of saturation concentration CR Contact recreation - WS Water supply - I Irrigation - IA Industrial abstraction - NS Natural state The natural quality of the water shall not be altered A Aesthetic - C Cultural purposes The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values ANZECC Guidelines The ANZECC (2000) guidelines provide trigger values for DO based on statistical analysis of regional monitoring data from reference sites in Australia and New Zealand (ANZECC, 2000; section ). The default trigger values in the ANZECC guidelines were derived from ecosystem data for unmodified or slightly-modified ecosystems supplied by state agencies. The choice of these reference systems was not based on any objective biological criteria. As such, the physical and chemical trigger values do not represent thresholds for adverse effects on the respective ecosystems. The trigger values in ANZECC (2000), which have been widely used in New Zealand up to now, but which were based on reference data supplied at the time of their compilation, are not appropriate as guidelines. Auckland Council WQI Both minimum and maximum DO saturation conditions are one of the seven water parameters incorporated into the Auckland Council WQI (minimum 74%, maximum Technical aspects of integrating water quality science in freshwater and coastal environments 27

38 120% saturation; (Lockie et al. 2013)), which is used as part of the SoE reporting (Auckland Council 2014b). The high DO saturation will be indicative of excessive algae or macrophytes present in that water body. DO levels between the minimum or maximum DO threshold should protect river-dwelling organisms. However, as described below, measurement times may not be representative of the most stressful conditions. National Objectives Framework With the advent of the NPS-FM, the Ministry for the Environment requested that NIWA outline a NOF for rivers to protect the value Ecosystem Health for the attributes: temperature, dissolved oxygen and ph. The NIWA authors reviewed the scientific information and approaches used overseas for setting DO guidelines. They identified several critical factors that should be considered when deriving DO criteria. Adequate consideration of these factors led them to propose substantial changes to DO guidelines in New Zealand: Lethal v. sub-lethal effects: Defining standards based solely on avoiding lethal effects will not be sufficient to protect ecosystem health. Sub-lethal impacts, for example on recruitment success or growth, may result in reduced abundance and eventual loss of more sensitive species and a shift in community composition to favour more tolerant (possibly exotic) species. Representativeness: Robust data on DO sensitivity must be available for a representative range of freshwater species (e.g., fish, macroinvertebrates, amphibians). Limited data are available regarding the DO tolerances of native NZ species, particularly macroinvertebrates. Consequently, those data were complemented by more detailed information on international species surrogates, including chinook salmon and rainbow trout, which are important recreational fish species in New Zealand. Together these provided a robust basis for establishing thresholds. Diel and seasonal variations (duration, magnitude and frequency of exposure): Guidelines must account not only for DO concentration minima, but also for the frequency and duration of these conditions. This includes accounting for natural fluctuations in dissolved oxygen concentrations. Multiple stressors: The impacts of low DO on aquatic organisms may be affected by the influence of additional stressors, e.g., water temperature, and which may therefore require special consideration. Concentration versus saturation: Specifying limits in the form of DO concentration (mg/l) was considered more appropriate than using saturation Technical aspects of integrating water quality science in freshwater and coastal environments 28

39 (as is currently used in the RMA). By defining a standard as a percentage of maximum saturation, the threshold DO concentration decreases as water temperature increases (i.e., 80% saturation at 10 C is 9.0 mg/l and at 25 C is 6.6 mg/l). The authors found this to be counter-intuitive for ecosystem protection purposes given that the oxygen demand of aquatic fauna generally increases with increasing temperature. This report generated specific NOF bands (A, B, C, D) for DO (Table 3-4), incorporating three statistics for discrete specified periods (1 and 7 days) over the summer. Setting limits for daily DO minima primarily provides protection against short duration exposure to DO concentrations that exceed the acute mortality thresholds of sensitive aquatic species. The longer term (7-day) averages should avoid chronic impacts as a consequence of continuous or regularly occurring low DO events. All three statistics must be met for each band. The NPS-FM 2014 (MfE 2014a), has adopted part of the above for DO in rivers below point discharges. We have no information as to the reason for the national standards being restricted to reaches downstream of point source discharges. No recommendation in this regard was provided in the reference document (Davies- Colley et al. 2013). Although further clarification may be provided in the forthcoming MfE implementation guidance, however, we recommend a more general application of the DO standards to streams and rivers where ecological habitat, including fish passage, are considered priority values for management. In the Attribute Tables (Appendix 2) the Narrative Attribute State is the same as in Table 3-4A. The numerical Attribute State includes two of the three statistics from Table 3-4B: the 7-day mean minimum (which is the mean value of 7 consecutive daily measurements) and the 1-day minimum (which is the lowest daily minimum across the whole summer period). Here the summer period has been redefined as 1 November to 30 April. The requirement for continuous monitoring over 7 day periods during critical seasons means that one-off spot measurements that have been used in the past are unlikely to have adequately described the DO regime of streams and rivers. In addition to the proposed guidelines, in aquatic ecosystems, temperature, DO and ph are closely interrelated. Therefore the authors describe how the attributes temperature, DO and ph may interact, and how to conduct continuous monitoring so that limits for these variables can be applied. Technical aspects of integrating water quality science in freshwater and coastal environments 29

40 Table 3-4 Proposed NOF for dissolved oxygen regime in rivers and streams (and groundwater, lakes and estuaries) in Maritime regions of New Zealand (Davies-Colley et al. 2013). A. Band descriptors NOF Band A B C D (unacceptable / does not provide for value) Band descriptors (narrative what will people notice as the impact on the value) No stress caused by low dissolved oxygen on any aquatic organisms that are present at matched reference (near-pristine) sites. Occasional minor stress on sensitive organisms caused by short periods (a few hours each day) of lower dissolved oxygen. Risk of reduced abundance of sensitive fish and macroinvertebrate species. Moderate stress on a number of aquatic organisms caused by dissolved oxygen levels exceeding preference levels for periods of several hours each day. Risk of sensitive fish and macroinvertebrate species being lost. Significant, persistent stress on a range of aquatic organisms caused by dissolved oxygen exceeding tolerance levels. Likelihood of local extinctions of keystone species and loss of ecological integrity. B. Numerical Values NOF Band 7-day mean a mg/l 7-day mean minimum mg/l 1-day minimum mg/l A/B b B/C C/D D <6.5 <5.0 < Relevance/suitability for Auckland In Auckland, as in other parts of New Zealand, low DO is probably most commonly encountered in warm, unshaded, slow-flowing, lowland rivers where aquatic plants or algae are abundant. These can occur in catchments dominated by pastoral, horticultural or urban land uses. In fact, DO concentrations in some lowland Auckland streams and rivers are falling below the recognised lethal thresholds for some fish species (Wilding et al. 2012), and large diel variations fall below the 4.0 mg/l 1-day minimum threshold in a stream in South Auckland, (Wilcock et al. 2001). Other sites in Auckland which may be susceptible to low DO concentrations may include: Technical aspects of integrating water quality science in freshwater and coastal environments 30

41 downstream of water supply dams where water is released from the hypolimnion groundwater dominated streams subjected to a large input of low DO groundwater upper estuarine river reaches (Williamson et al. 2016; Wilding et al. 2012) downstream of point sources of pollution with a high organic content. DO is measured monthly at 34 river and stream sites for SoE monitoring, (Lockie et al. 2013). The low DO threshold (74%) is exceeded at 41% of sites and the high threshold (120%) at 6% of sites Conclusions/Recommendations Recommendations for DO guidelines for Auckland is premature until MfE have finalised DO attributes in the NOF. However, even when these are available, their applicability to all Freshwater Management Units, especially small, lowland rural and urban streams, would need to be critically assessed for the Auckland region. The proposed NOF guidelines require far greater monitoring effort than is usual when measuring DO in streams and rivers. The greater monitoring requirement may require equipment that can be deployed remotely for periods of up to 7 days. Details are available on continuous monitoring of dissolved oxygen in a recent DO report commissioned through the National Environmental Monitoring Standards (NEMS) process (Wilcock et al. 2013). Procedures for processing and assessing DO data will need to be developed and put in place to expedite reporting. The proposed NOF guidelines have a requirement for continuous monitoring during critical times and seasons. Irrespective of the outcome of the MfE review and final specification of NOF bands for DO, current approaches to assessing compliance (e.g., RMA Schedule 3, or AC s WQI) should at least focus on the same critical conditions. The most critical time for dissolved oxygen stress is likely to be under summer low flows when water temperatures are high. The significant diel variations that can occur in dissolved oxygen concentrations means continuous monitoring is needed. The proposed NOF bands would be appropriate for the values: aquatic ecosystem, fisheries, fish spawning, aquaculture, mahinga kai and natural waters. Technical aspects of integrating water quality science in freshwater and coastal environments 31

42 3.3 Salinity and conductivity Overview/Issues Salinity or electrical conductivity (EC) are measures of the total dissolved solids (TDS) concentration of inorganic ions (salts) in the water. Salinity is used to measure the total ion (salt) concentration (mainly Na + and Cl -, but also Ca 2+, Mg 2+, K +, CO 3 2- and SO 4 2- ) in estuarine and marine waters, with ocean waters having a salinity around 35 parts per thousand ( ). EC is used to measure the total ion concentration in fresh and brackish waters. Freshwaters are generally considered to have an EC of less than 1000 μs/cm. Measures of salinity and EC indicate whether the chemical nature of aquatic ecosystems is being altered and provides a warning of the potential loss of native biota. Salinity changes may affect aquatic organisms in two ways: direct toxicity through physiological effects both increases and decreases in salinity can have adverse effects, and indirectly by modifying the species composition of the ecosystem and affecting species that provide food or refuge. Salinity in freshwaters is an issue for water potability (for humans), stock water and irrigation, and there are guidelines for salinity or conductivity for these uses (see Appendix B) Use/applicability/importance Salinity increases or decreases are not generally an issue in NZ as they are in Australia. Flow abstraction from streams will result in increased upstream penetration of the tidal saline water (termed saline wedge ), which may potentially affect abstractive use in lower reaches Critique/review of existing and proposed approaches to salinity management/guidelines A summary of existing numerical guidelines is available in Appendix Table B2. Schedule 3 RMA Schedule 3 has narrative standards that would cover salinity issues for water supply and irrigation, but no explicit numerical standards (Table 3-5). Technical aspects of integrating water quality science in freshwater and coastal environments 32

43 Table 3-5 Standards for Water Quality Classes for salinity from Schedule 3 RMA. Class Purpose Criteria AE Aquatic ecosystem - F Fisheries - FS Fish spawning - SG Gathering or cultivating of shellfish - CR Contact recreation - WS Water supply The water shall not be tainted or contaminated so as to make it unpalatable or unsuitable for consumption by humans after treatment (equivalent to coagulation, filtration, and disinfection), or unsuitable for irrigation. I Irrigation The water shall not be tainted or contaminated so as to make it unsuitable for irrigation of crops growing or likely to be grown in the area to be irrigated. IA Industrial abstraction - NS Natural state The natural quality of the water shall not be altered A Aesthetic - C Cultural purposes The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values ANZECC Guidelines ANZECC (2000, their chapters , ) has recommendations and guidance for deriving trigger values for salinity from reference conditions. For important ecosystems, where an appropriate reference system(s) is available and there are sufficient resources to collect the necessary information for the reference system, the low-risk trigger concentrations for EC (or salinity) should be determined as the 20%ile or 80%ile of the reference system(s) distribution, depending upon whether low salinity or high salinity effects are being considered. Other percentiles can be chosen for more highly impacted systems. Salt tolerance is highly variable for different plants and tolerances are described in ANZECC (2000) for irrigation requirements. Technical aspects of integrating water quality science in freshwater and coastal environments 33

44 US Environmental Protection Agency (US EPA) The US EPA have promulgated a region-specific conductivity guideline of 300 μs/cm to apply to Appalachian streams that are dominated by calcium and magnesium salts of sulphate and bicarbonate at circum-neutral to mildly alkaline ph (US EPA 2011). Research is currently being undertaking to determine whether conductivity criteria are suitable for application to streams and rivers in other US regions (W. Clements, Colorado State University, pers comm.). Although conductivity was found to be a highly significant discriminator of macroinvertebrate communities in a study of 88 New Zealand rivers (Quinn et al. 1990a), further work is required to determine whether conductivity could provide useful effects-related bands and whether these would be applicable to Auckland streams. NZ Drinking Water Standards The New Zealand Drinking Water Standards also offer guidance for aesthetic characteristics of drinking water. These include guidelines for chloride (250 mg/l), sodium (200 mg/l), and total dissolved salts (1000 mg/l) Relevance/suitability for Auckland Conductivity and salinity is currently measured monthly at 34 river and stream sites for SoE monitoring, but these parameters are not one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). Only one site has a particularly high salinity (Otaki, median 0.14, maximum 2.38 in 2012), probably indicating saline intrusion. Salinity changes are not generally an issue in Auckland. In surface waters, it is probable that the only significant salinity changes are related to changes in freshwater flow regimes into estuaries after land use change. This may bring about changes in biota (e.g., this may have been the reason for observed changes in foraminifera taxa (Hayward et al. 2006)). Estuaries are subject to highly variable salinity changes because of highly variable freshwater flows so it is difficult to recommend allowable deviations from reference conditions for variable inflow conditions. Salinity may become an issue in some parts of Auckland in aquifers close to the coast that are used for drinking water supplies or irrigation. Guidance for drinking (human and stock) waters are provided as described above Conclusions/Recommendations The guidelines described above are appropriate for salinity in drinking water and for salt tolerance for irrigation of plants. At present we are unaware of salinity changes likely to be of consequence for aquatic organisms. If changes of significance are Technical aspects of integrating water quality science in freshwater and coastal environments 34

45 identified in the future, we recommend the ANZECC guidelines approach is followed, where the allowed changes are specified as proportional changes from reference conditions (e.g., 20%). 3.4 ph The following was largely based on National Objectives Framework - Temperature, Dissolved Oxygen & ph. Proposed thresholds for discussion by Davies-Colley et al. (2013) Overview ph is a property of freshwaters that affects many other water quality variables. Therefore, data on ph are needed to interpret the aqueous toxicities of ammonia, toxic metals and organic compounds. Additionally, although fish and invertebrate species demonstrate a wide range of tolerances and preferences to different ph ranges, there is common agreement that a ph range of 6-9 is needed to prevent excessively acidic or alkaline conditions which are likely to adversely affect freshwater ecosystems. In many streams with abundant plant biomass (macrophytes, phytoplankton or periphyton), during periods of base flow strong diel cycles of DO and ph regularly occur as a consequence of the uptake and release of oxygen and carbon dioxide by the plants. Maxima in ph and DO occur in the late afternoon when photosynthesis dominates whereas minima occur in early morning when respiration is dominant Use/applicability/importance ph is a property of freshwaters that affects many other water quality variables. Therefore data on ph, preferably continuous records defining ph regime, are needed to interpret other variables. The aqueous toxicities of ammonia, toxic metals and organic compounds are affected by ph. ph toxicity per se is rarely an issue. However, it may be an issue in streams with high macrophyte or periphyton biomass, along with DO and temperature (see above) Critique/review of existing and proposed approaches to salinity management/guidelines A summary of existing numerical guidelines in available in Appendix Table B2. Schedule 3 RMA Schedule 3 specifies ph Standards for Class AE waters, but ph guidelines are also implicit in the narrative standards for Class CR, NS and C waters (Table 3-6). Technical aspects of integrating water quality science in freshwater and coastal environments 35

46 Table 3-6 ph Standards for Water Quality Classes from Schedule 3 RMA. Class Purpose Criteria AE Aquatic Ecosystem The following shall not be allowed if they have an adverse effect on aquatic life: any ph change F Fishery - FS Fish Spawning - SG Gathering/Cultivating Shellfish - CR Contact Recreation The water shall not be rendered unsuitable for bathing by the presence of contaminants WS Water supply The ph of the water shall be within the range 6.0 to 9.0 units I Irrigation - IA Industrial Abstraction - NS Natural State The natural quality of the water shall not be altered. A Aesthetic - C Cultural The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values ANZECC Guidelines The ANZECC (2000) guidelines provide trigger values for ph based on statistical analysis of regional monitoring data from reference sites in Australia and New Zealand (ANZECC, 2000; section ). The default trigger values in the ANZECC guidelines were derived from ecosystem data for unmodified or slightly-modified ecosystems supplied by state agencies. The choice of these reference systems was not based on any objective biological criteria. As such, the physical and chemical trigger values do not represent thresholds for adverse effects on the respective ecosystems. NPS-FM The Ministry for the Environment requested that NIWA outline a NOF for rivers to protect the value Ecosystem Health for the attributes: temperature, dissolved oxygen and ph. The NIWA authors reviewed the scientific information and overseas approaches to setting ph guidelines. A NOF for ph is proposed (Table 3-7) built on a Technical aspects of integrating water quality science in freshwater and coastal environments 36

47 gradient of increasing stress from the no effect A grade to significant loss of ecological integrity at D grade. The framework should apply throughout the diel (24- hour) regime of ph measurements and not just to the narrower range of daytime spot measurements that are commonly reported. This will require more extensive use of continuous ph monitoring. The standards proposed in Table 3-7 are drawn from a comparatively few experimental and field observations of New Zealand fish and invertebrate species, as well as international standards, guidelines and trigger values based on a mixture of observations and statistical inferences. The values in Table 3-7 are typical of many guidelines and standards throughout the world. Table 3-7 Proposed NOF for ph regime in rivers and streams (and groundwater, lakes and estuaries). The term regime refers to the diel fluctuation of ph. (Davies-Colley et al. 2013). NOF Band A B C D (unacceptable / does not provide for value) Band descriptors (narrative what will people notice as the impact on the value) No stress caused by acidic or alkaline ambient conditions on any aquatic organisms that are present at matched reference (near-pristine) sites. Occasional minor stress caused by ph on particularly sensitive freshwater organisms (viz. fish and insects). Stress caused on occasion by ph exceeding preference levels for certain sensitive insects and fish for periods of several hours each day. Significant, persistent stress caused by intolerable ph on a range of aquatic organisms. Likelihood of local extinctions of keystone species and destabilisation of river ecosystems. Summer monitoring data upper 95 th percentile 6.5 < ph < < ph < < ph < 9.0 ph < 6 or ph > Relevance/suitability for Auckland Monitoring results (e.g., Auckland SoE monitoring) have suggested that ph toxicity per se is rarely an issue. The ph is currently measured monthly at 34 river and stream sites for SoE monitoring, with a requirement of values to be between 6.4 and 8.1 for this parameter as one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). The low ph threshold is not exceeded and the high threshold exceeded at only one of the sites. However, it may be an issue in streams with high macrophyte or periphyton biomass, along with DO and temperature conditions which occur reasonably commonly Technical aspects of integrating water quality science in freshwater and coastal environments 37

48 throughout Auckland s developed lowlands (see above). Greater variation in ph may be expected if continuous monitoring were to be used for measurement. It is important to measure ph (and if necessary manage it) when assessing ammonia toxicity and it may be useful when assessing heavy metal toxicity. If the Biotic Ligand Model is used to determine toxicity of Cu and Zn, then ph will need to be measured along with other general water quality characteristics Conclusions/Recommendations The natural variation of ph is well understood and is captured in the attribute tables proposed for incorporation into future NOF standards (Davies-Colley et al. 2013). The proposed NOF bands are similar or slightly more rigorous than guidelines used in the past. However, management of this attribute for ecosystem health (and other related values such as fisheries, fish spawning, aquaculture, mahinga kai, natural waters) will require more rigorous monitoring (continuous over summer) than was typically undertaken in the past (spot measurements at infrequent time intervals e.g., monthly). This requirement would place a greater burden on monitoring programmes. Limit-based approaches can be developed with ph using mass balance of the cations, anions and organic acids that determine ph. This may be applied to macrophyte-dominated streams with ph changes driven by photosynthetic activity (Wilcock et al. 2005), or point source discharges using stoichiometry calculations based on discharge and receiving water ph and alkalinity measurements. However, we are not aware of active concern for ph and its management in Auckland, and so application of the limit-based approach is possibly not necessary. Should it be necessary for management to address ph then we recommend that a critical review is undertaken before committing to more-rigorous ph monitoring. 3.5 Water clarity (and colour) Overview Water clarity and underwater visibility is important for recreational activities such as swimming and water-skiing. To minimise risk of injury while swimming, you should be able to see at least 1.6 metres underwater. It is also important from an aesthetic point of view most people prefer to see clear water in our rivers and lakes. Clarity also impacts on ecology in a number of ways, including: directly affecting visual acuity for both predators and prey directly impacting on food quality for filter and particle feeders via the concentration, physical, chemical and biological characteristics of the particles that determine clarity. Technical aspects of integrating water quality science in freshwater and coastal environments 38

49 3.5.2 Use/applicability/importance Public perception of water quality is dominated by visual and aesthetic factors (MfE 1994). Colour and clarity have been specifically protected by the Resource Management Act - there will be no change in colour or visual clarity following the discharge of contaminants. Substances which alter clarity can also affect aquatic life. Clarity and turbidity are interchangeable - the value of one can be calculated from the other once their relationship has been established for a specific water body Critique/review of existing and proposed approaches to water clarity management/guidelines Existing numerical guidelines are summarised in Appendix Table B2. Schedule 3 RMA Schedule 3 of the RMA only specifies clarity for CR waters, but clarity criteria are implicit in Class NS, A and C Waters (Table 3-8). Table 3-8 Standards for Clarity (turbidity) for Water Quality Classes from Schedule 3 RMA. Class Purpose Criteria AE Aquatic Ecosystem - F Fishery - FS Fish Spawning - SG Gathering/Cultivating - Shellfish CR Contact recreation The visual clarity of the water shall not be so low as to be unsuitable for bathing WS Water supply - I Irrigation - IA Industrial abstraction - NS Natural state The natural quality of the water shall not be altered. A Aesthetic The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified aesthetic values C Cultural The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values ANZECC Guidelines The ANZECC (2000) guidelines provide trigger values for turbidity based on statistical analysis of regional monitoring data from reference sites in Australia supplied by state agencies and for New Zealand sites (Davies-Colley 2000). The New Zealand values for clarity and turbidity for upland and lowland rivers are Technical aspects of integrating water quality science in freshwater and coastal environments 39

50 provided in Appendix B (Table B2). These have no human perception or biological basis. MfE Guidelines MfE water quality guidelines for clarity and colour are summarised in Table 3-9, in terms of recreation in New Zealand freshwater and marine systems. Similarly, there are guidelines for Total Suspended Solids (TSS) and turbidity for freshwaters with respect to water clarity. Table 3-9 Water quality guidelines for clarity in use in New Zealand (from Waters of New Zealand (Davies-Colley et al. 2004)). Optical variable Rationale Guideline Reference Suspended sediment Turbidity Aesthetics and contact recreation Aesthetics and contact recreation <4 mg/l (Smith et al. 1993) < 2 NTU (Smith et al. 1993) Visual clarity (black disk visibility) Aesthetics and aquatic life <20-50% change (depending on water class, site conditions) (MfE 1994) Visual clarity (black disk visibility) Contact recreation >1.6 m (MfE 1994) Light penetration Light for photosynthesis < 10% change in euphotic depth, <20% change in lighting at bed (MfE 1994) Colour Aesthetics <5 or 10 Munsell units change (depending on water class) (MfE 1994) Auckland Council WQI Turbidity is currently measured monthly at 34 river and stream sites for SoE monitoring, with a requirement for turbidity to be less than 33 NTU. Existing guideline advantages and limitations Guidelines for clarity and optical characteristics have been in use for several decades, are reasonably robust and are widely accepted. This partly stems from the early guidance in the 1991 RMA that there will be no change in colour or visual clarity following the discharge of contaminants. It is likely that this will be a key attribute for the values primary and secondary contact recreation and aquatic Technical aspects of integrating water quality science in freshwater and coastal environments 40

51 ecosystems in the Auckland region, as well as other values that involve the continued viability of aquatic organisms. While guidelines have been derived to protect phytoplankton and periphyton growth, the existing guidelines do not recognise the importance of visual sighting range for predatory animals and their prey. However, the clarity guidelines which are based on human visual perception of water quality and providing safety during water recreation, will partly address this ecological requirement. It will be challenging to develop a limits-based approach for clarity by itself, based on catchment models, because of the complexity of the processes that determine particle behaviour and hence their effects on the optical properties of water Relevance/suitability for Auckland Turbidity is currently measured monthly at 34 river and stream sites for SoE monitoring as one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). The NTU threshold is exceeded for 56% of sites. Suspended sediment concentration is also measured as part of the monthly monitoring. Visual clarity (black disk) measurements are not undertaken as part of the current SoE monitoring programme. Suspended sediment is a major contaminant in Auckland waters and hence has a large bearing on clarity and appearance of its waters, as well as it effects of visual acuity for sighted aquatic organisms. In this respect, suspended sediment is relevant to recreation, aquatic ecosystem, natural form and character, aesthetics, and mahinga kai. It is also indirectly related to water potability, irrigation and industrial use, but this is discussed under Total Suspended Solids (TSS) in the next section. Light penetration may be of importance for primary productivity, especially in hardbottomed streams and in the near-pristine lakes in the Auckland region Conclusions/Recommendations Because clarity is a major factor in the public perception of water quality it will be also important in natural form and character and mahinga kai. Reference sites should be used to establish clarity ranges in natural environments. This attribute will be relevant across all surface waters. The strong relationship between colour, clarity and suspended sediments require these variables to be considered together in order to achieve water quality values. Technical aspects of integrating water quality science in freshwater and coastal environments 41

52 3.6 Total Suspended Solids Overview Fine sediment occurs naturally in rivers and streams. It usually enters a stream because of terrestrial weathering processes, bank erosion, and in-stream fluvial processes. Sediment particles are transported and deposited in streams and their receiving waters, such as lakes, estuaries and coastal bays, as the result of surface water movement across the landscape. Human development of land and water channels in watersheds can greatly increase the amount of fine sediment entering fluvial systems. This can be caused by disturbing land vegetation cover, increasing rain-runoff rates and volumes, increasing flow velocities in channels and by placing structures in channels. Excessive concentrations of TSS decrease clarity and therefore affect ecosystems and recreational use (as described above). Excessive loads of particulate material can increase the amount of fine sediment in the beds of rivers and streams, depending on the hydraulic energy of the system. In extreme cases, the volume of sediment can overwhelm the transport capabilities of the fluvial system, which result in deposition of fine sediments on the bed of streams and rivers. This will certainly occur in lower-energy receiving waters such as lakes and estuaries, where infilling and shallowing results. Managing TSS impacts requires a two-pronged approach, involving two sets of guidelines: Clarity guidelines, which were described in Section 3.5. Sedimentation guidelines, described fully in this section Use/applicability/importance TSS guidelines would be used to manage the impacts associated with deposition of terrigenous sediment derived from erosion on stream and river bed sediment texture Critique/review of existing and proposed approaches to water clarity management/guidelines A summary of existing numerical guidelines is available in Appendix Table B2. Schedule 3 RMA Schedule 3 specifies narrative deposition criteria only for AE waters, which are implicit in class NS, A and C Waters (Table 3-10). Technical aspects of integrating water quality science in freshwater and coastal environments 42

53 Table 3-10 Standards for Total Suspended Solids (TSS) for Water Quality Classes from Schedule 3 RMA. Class Purpose Criteria AE Aquatic ecosystem The following shall not be allowed if they have an adverse effect on aquatic life: any increase in the deposition of matter on the bed of the water body or coastal water SG Gathering/Cultivating - S Shellfish - CR Contact recreation The visual clarity of the water shall not be so low as to be unsuitable for bathing WS Water supply - I Irrigation - IA Industrial abstraction - NS Natural state The natural quality of the water shall not be altered A Aesthetic The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified aesthetic values C Cultural The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values TSS are also relevant to values associated with water supply, irrigation and industrial abstraction, and to some extent, stock watering. High levels of TSS can block pipes and nozzles, and greatly increase the cost of water treatments (e.g., flocculation/filtration in water supplies). However, no accepted published guidelines are used across New Zealand. ANZECC Guidelines TSS criteria are not covered in ANZECC (2000), with the exception of indicative aquaculture guidelines. National guidelines for hard-bottomed streams Numerical guidelines for fine sediments in the beds of freshwater systems have only recently become available for hard-bottomed streams in New Zealand (Clapcott et al. 2011). This study investigated published and unpublished methods for measuring sedimentation in streams and rivers, and in the process defined guidelines, which can be further refined depending on site characteristics. The guidelines for sediment deposition and accumulation were defined for each measurement method (Table 3-11A and 3-11B). Additional guidelines for salmonid spawning sites are not shown here. Technical aspects of integrating water quality science in freshwater and coastal environments 43

54 Table 3-11A Description of methods for assessing the effects of fine sediment deposition. Sediment Component Method Metric Description Sediment cover Bankside visual % sediment cover A bankside semi-quantitative measure of the relative cover of fine sediment in comparison to other substrate classes In-stream visual % sediment cover An in-stream (using an underwater viewer) semiquantitative measure of the relative cover of fine sediment in comparison to other substrate classes Substrate size Wolman pebble count % sediment ( W2 ), d16, d50, d86 A quantitative measure of the percent of fine sediment calculated from at least 100 random substrate measurements Interstitial space Quorer SIS (mg/m 2 ), SOS (mg/m 2 ) A quantitative measure of the amount of suspendable inorganic sediment (SIS) and suspendable organic sediment (SOS) on the streambed Shuffle index Shuffle index score A qualitative rank (1-5) measure of the degree of suspendable fine sediment on the streambed Sediment depth Depth (mm) A quantitative measure of the depth of fine sediment in runs Table 3-11B Recommended guidelines for assessing the effects of deposited fine sediments on the in-stream values of hard-bottomed streams. Sediment measure Numerical Value Method Value =Biodiversity Sediment cover <20% or within 10% cover of reference site Bankside or instream visual Substrate size <20% or within 10% cover of reference site Wolman pebble count Suspendable sediment <450 g/m 2 Quorer (SIS) Value = Amenity Sediment cover <25% Bankside or instream visual Suspendable sediment <3 Shuffle index Technical aspects of integrating water quality science in freshwater and coastal environments 44

55 Although very new, the sedimentation guidelines (Table 3-11B) were based on an extensive scientific experience, literature review and testing by research scientists and regional councils throughout New Zealand. Therefore, they are likely to be reasonably robust, but could be refined further to incorporate experience obtained following their application. Although these guidelines will have little applicability to soft-bottomed streams and rivers, this does not mean that soft-bottomed streams are not susceptible to impacts from increased sedimentation of fine sediments. From an ecological standpoint, while animals that live in fine sediments are adapted to that environment, it does not mean that they can deal with higher rates of fine sediment inputs than they are accustomed to. Freshly-deposited fine sediments may also present a different matrix to existing sediment dwelling animals (e.g., less cohesive). Similarly, from an amenity standpoint, in situ fine sediments may have quite different physical properties to freshly-deposited fine sediment; for example, the latter may be more easily suspended. However, there are no comparable guidelines for fine sediment deposition in soft-bottomed streams. NPS-FM MfE has recently (July 2016) commissioned further work to establish suspended sediment and deposited sediment thresholds suitable for implementation in the NPS- FM. As yet, such guidelines cannot be related to sediment loads in the waterways. It is likely however, that relationships between deposition/accumulation and sediment inputs from the watershed could be developed. If this occurs, then it will be possible to define limits for the magnitude of erosion from developing and developed catchments. Application of advanced catchment runoff models that quantify the benefits of management intervention (such as enhanced CLUES), would help determine the catchment management strategies and erosion control techniques required to meet the limits Relevance/suitability for Auckland TSS is currently measured monthly at 34 river and stream sites for SoE monitoring, but this parameter is not one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). The sedimentation guidelines are highly relevant to the protection of hard-bottomed streams and provide numerical guidance for the RMA narrative standard for Aquatic Ecosystems The following shall not be allowed if they have an adverse effect on aquatic life: any increase in the deposition of matter on the bed of the water body or coastal water. They will also provide guidance for protection of aesthetic, cultural Technical aspects of integrating water quality science in freshwater and coastal environments 45

56 and natural values from excessive sedimentation or accumulation. They will have little applicability to predominantly soft-bottomed streams and rivers Conclusions/Recommendations Given the importance of sediment impacts in the Auckland region, the relative rarity of hard-bottomed streams, and the near-pristine environments in which many of these streams occur (Hunua Ranges, Waitakere Ranges, Great Barrier Island) the guidelines for sedimentation (Clapcott et al. 2011) should be a primary management tool (in NOF language a key attribute) for these aquatic environments. This attribute is applicable to the values fish spawning, aquatic health, natural state, aesthetics/visual character. We recommend that further work be undertaken to establish thresholds for depositional sediment effects in soft-bottomed streams in the Auckland region. Monitoring of sedimentation in soft-bottom streams should be undertaken with comparison with suitable reference conditions. Technical aspects of integrating water quality science in freshwater and coastal environments 46

57 4 Nutrient Enrichment 4.1 Overview of Eutrophication in New Zealand Excessive nutrient concentrations in waterways can cause eutrophication, resulting in nuisance plant growth as periphyton or macrophyte cover in rivers. In lakes, it can be summer blooms of phytoplankton, which can form surface scums, mass algal dieoff causing oxygen depletion and in extreme cases, rotting vegetation on lake shores. In addition, what is becoming more frequent are increases in the incidence and severity of harmful blooms such as toxic algae (cyanobacteria, blue-green algae). An increasing number of cyanobacteria species are known to include toxinforming strains. These natural cyanotoxins are a threat to humans and animals when consumed in drinking water, through consumption of the bacteria by planktonic or surface film feeders or following direct dermal contact. In rivers and streams, plant growth at any depth depends on sufficient light at that depth. Shade provided by overhanging vegetation or on rare occasions by landscape (canyons), or in deeper rivers by turbidity, will limit plant growth in rivers. Turbidity can also limit growth in shallow lakes where bottom sediments can be resuspended by wind or fish (e.g., koi carp). Flow also limits plant growth. Steep, upland streams with high velocities are less susceptible to plant growth, although periphyton is well-adapted to attachment to cobbles. Toxicity associated with the specific form of nutrients (e.g., nitrate and ammonia), are dealt with elsewhere (Section 5). 4.2 Use/applicability/importance Enrichment of fresh waters is a major problem in New Zealand, chiefly because of farming and horticulture, but especially dairy farming. Nuisance growths of periphyton are commonly encountered in summer, and phytoplankton blooms are endemic in enriched lakes. Problems with BOD are largely associated with pointsource discharges; adverse effects associated with these have in general been managed successfully with discharge consents. Cyanobacteria blooms have occurred in NZ lakes since the 1970 s. However, the blooms have become an increasing problem in recent decades, possibly due to climate change and an increase in anthropogenic eutrophication (Ministry for the Environment and Ministry of Health 2009). Planktonic cyanobacteria are known to produce a range of cyanotoxins, which can be toxic to humans and animals usually during bloom conditions, through ingestion in drinking water or through direct contact. The contact route is exacerbated when a combination of blooms and wind Technical aspects of integrating water quality science in freshwater and coastal environments 47

58 form surface scums near sites where recreation occurs or where good access to water is afforded. 4.3 Critique/review of existing and proposed approaches to nutrient enrichment management/guidelines There are a large number of guidelines for nutrient enrichment in New Zealand. A summary of existing numerical guidelines is available in Appendix Table B RMA Schedule 3 Schedule 3 has narrative standards regarding undesirable biological growths for Class AE, FS, CR, WS, I and IA waters, but because eutrophication can have a profound effect on water quality, these standards are implicit for Class NS, A and C Waters (Table 4-1). Table 4-1 Standards for Eutrophication for Water Quality Classes from Schedule 3 RMA. Class Purpose Criteria AE Aquatic ecosystem There shall be no undesirable biological growths as a result of any discharge of a contaminant into the water. F Fisheries FS Fish spawning There shall be no undesirable biological growths as a result of any discharge of a contaminant into the water. SG Gathering/Cultivating shellfish - - CR Contact Recreation There shall be no undesirable biological growths as a result of any discharge of a contaminant into the water WS Water supply There shall be no undesirable biological growths as a result of any discharge of a contaminant into the water. I Irrigation There shall be no undesirable biological growths as a result of any discharge of a contaminant into the water. IA Industrial abstraction There shall be no undesirable biological growths as a result of any discharge of a contaminant into the water NS Natural state The natural quality of the water shall not be altered A Aesthetics The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified aesthetic values C Cultural The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values Technical aspects of integrating water quality science in freshwater and coastal environments 48

59 4.3.2 ANZECC The ANZECC (2000) guidelines also provide trigger values for nutrients and chlorophyll a based on statistical analysis of regional monitoring data from reference sites in Australia and New Zealand (ANZECC, 2000; section ). The default trigger values in the ANZECC guidelines were derived from ecosystem data for unmodified or slightly-modified ecosystems supplied by state agencies. The choice of these reference systems was not based on any objective biological criteria. As such, the physical and chemical trigger values do not represent thresholds for adverse effects on the respective ecosystems. The ANZECC trigger values have been widely used, but should have had little relevance to NZ because they are based on comparisons with reference conditions, where the reference conditions are default values which may have little relevance. This approach would have limited use in Auckland s freshwaters (however, this approach is recommended for marine waters Williamson et al. 2016) MfE Guidelines Nutrient guidelines for nuisance growths in rivers have been published in New Zealand by MfE (1992, Table 4-2). Table 4-2 Water quality guidelines used in New Zealand for nutrients (MfE 1992). Nutrient Rationale Numerical values Dissolved inorganic nitrogen Nuisance periphyton growth <4 10 µg/l (depending on accrual time) Dissolved reactive phosphorus Nuisance periphyton growth µg/l 5-day Biochemical oxygen demand (BOD) Nuisance bacterial slime growth <5 mg/l Lake Trophic Index and Rotifer Index Nutrient concentrations, water clarity and algal levels determine a lake s trophic state which in turn reflects how well a shallow lake can support native freshwater plants and animals. The Lake Trophic Index (LTI) of a lake is calculated for each of the four trophic indicators: chlorophyll a (Chla); Secchi depth (SD); total nitrogen (TN), and total phosphorus (TP). These are combined to calculate a lake eutrophication grading. The LTI is described more fully in section 13. Related to the TLI is the Rotifer TLI. Rotifer assemblages in lakes reflect the trophic condition, effectively integrating chemical, physical and biological states and Technical aspects of integrating water quality science in freshwater and coastal environments 49

60 processes. It is claimed that these are easier and cheaper to measure, and have been applied in Auckland (Fowler and Duggan 2009). The TLI and rotifer TLI have been used to classify Auckland lakes and provide guidance for their management. The application of national standards and bottom lines (TN, TP and cyanobacteria) would provide a similar service for their management, but may result in some shifts in priorities. It would still be necessary to measure DO, turbidity, clarity and LakeSPI Auckland Council WQI Concentrations of total and dissolved nutrients (nitrogen and phosphorus) are currently measured monthly at river and stream sites for SoE monitoring, with a requirement that total phosphorus values be less than 0.09 mg P/L and total nitrogen values be less than 0.8 mg N/L for these parameters as two of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). The requirements are based on reference stream conditions and do not necessarily relate to biological effects. Concentrations of soluble reactive phosphorus, total Kjeldahl nitrogen, total oxidised nitrogen (nitrate + nitrite) and ammoniacal-nitrogen are also measured in the monitoring programme National Policy Statement for Freshwater Management The NPS-FM specifies guidelines for phytoplankton, TP and TN in lakes, cyanobacteria for lakes and lake-fed rivers, and periphyton in rivers. The NOF numeric standards are provided in Appendix B (Table B2) and the original NOF narrative and numeric standards are reproduced in Appendix D. These are all relevant to lakes and hard-bottomed streams Freshwater Management Units in Auckland. Nutrient loading rates (limits) are an important management metric because they provide a better measure of the nutrients in a system than do nutrient concentrations. Nutrients can be rapidly cycled through ecosystems and stored in/released from sediments and macrophytes in these circumstances, nutrient concentrations provide a snapshot of the nutrient dynamics, rather than the mass of material in the management unit. Nutrient loads are more relevant to lakes (accumulating systems) than streams (flow through systems) Soft-bottomed streams Macrophytes, including choking emergent vegetation are a much more common problem in lowland streams, especially in pastoral settings (e.g., South Auckland (Wilcock et al. 2001), Kumeu-Kaipara River (Diffuse Sources Ltd 2008)). Their occurrence and density is probably more a result of light climate (lack of shading by riparian vegetation) than nutrient enrichment. The combined effects of enriched Technical aspects of integrating water quality science in freshwater and coastal environments 50

61 sediment and associated nutrients, elevated temperature and reduced flows are all likely to be contributory factors (Matheson et al. 2012). Macrophytes are able to obtain nutrients from water and from river bed sediments, and they can proliferate even when water column nutrient concentrations are low when other conditions are favourable. 4.4 Relevance/suitability for Auckland Concentrations of total and dissolved nutrients (nitrogen and phosphorus) are currently measured monthly at 34 river and stream sites for SoE monitoring (Lockie et al. 2013). The P threshold (0.09 mg P/L) is exceeded at 68% of sites and the N threshold (0.8 mg N/L) at 74% of sites. However, enrichment of rivers in Auckland is not generally recognised as a widespread problem. This is partly due to the predominance of soft-bottomed streams, which have limited substrate suitable for periphyton growth. Although many of the hard-bottomed streams occur in relatively low nutrient situations (Waitakere and Hunua ranges), the NOF periphyton guidelines will be applicable. Auckland s lakes exhibit a wide range of trophic conditions. Seven routinely monitored lakes show trophic states that range from Mesotrophic to Hypertrophic (ARC 2008). LakeSPI, a measure of exotic and native vegetation in lakes, is a good metric of lake condition, including enrichment, as described in Section 11. Management of nutrient enrichment is important, and so NOF standards are likely to be highly relevant to Auckland. Auckland s urban streams provide sufficient nutrients to enable periphyton or macrophytes to proliferate where flow, substrate and light climate are suitable. Periphyton blooms along concrete channels may be of benefit by providing habitat and enabling contaminant processing. 4.5 Recommendations Nutrient enrichment resulting in periphyton blooms is not a major issue in Auckland rivers. In Auckland s hard-bottomed streams, focus should be on maintaining or providing riparian cover and shade. Their management can be guided by the NOF for periphyton. Addressing the response of nutrient enrichment in this way would be beneficial to the values: aquatic ecosystem, fisheries, fish spawning, aquaculture, mahinga kai and natural waters. In soft-bottomed streams the combined effects of: high light (i.e., no riparian shading), nutrient-rich sediment, elevated temperature and low flow may exacerbate macrophyte and emergent plant growths. It is difficult to recommend appropriate nutrient guidelines for soft-bottomed streams. Technical aspects of integrating water quality science in freshwater and coastal environments 51

62 In these conditions, macrophytes can be a major issue choking rivers, reducing DO levels, reducing fish habitat and providing habitat for noxious weeds. The proliferation of plants in the channel will also reduce the stream capacity and increase the flood risk for surrounding land. However, they can also be seen as beneficial by trapping sediment and reducing visible turbidity, providing cover for fish, reducing temperatures and processing contaminants. Managing macrophytes by skilful shade planting is recommended, where the positive and negative factors are balanced, resulting in partial weed growth (e.g., (Kumeu River (Diffuse Sources Ltd 2008), lowland Waikato River eel and whitebait habitat (NIWA 2010)). Studies are required to determine optimum planting strategy and hence guidelines. As with periphyton in hard-bottomed streams, management of the effects of nutrients in this manner would be beneficial to the values: aquatic ecosystem, fisheries, fish spawning, aquaculture, mahinga kai and natural waters. Nutrient enrichment is a major issue for many Auckland lakes. Applying NOF standards for TN and TP will probably classify many lakes D, so the implications of this will need to be addressed by council. The NOF cyanobacteria bands will provide guidance to prioritise management; when combined with the use of LakeSPI, the values primary and secondary recreation; fish spawning, aquaculture, mahinga kai and natural waters would be addressed. Methods and protocols employed in current SoE monitoring programmes are appropriate, and the existing database will provide adequate reference conditions. Nutrient enrichment may increase available N and P in sediments (as well as potentially toxic ammonia). At present, no criteria for N and P in concentrations in sediments exist. Inclusion of their measurement in management programmes may lead to development of useful criteria. Nutrient concentrations in sediments are also potentially amenable to a catchment-specific limits-based approach. The CLUES model is an integrated catchment based model that uses a GIS framework and is designed to assist policy makers in understanding the implications of land use scenarios for water quality and a range of other indicators (Harris et al. 2009). Technical aspects of integrating water quality science in freshwater and coastal environments 52

63 5 Toxicants in Surface Waters 5.1 Introduction A large number of commonly used anthropogenic chemicals may potentially be discharged to surface water from stormwater, farm runoff and wastewater. Toxic effects may be exerted in the water column through a multitude of mechanisms. The water column toxicants of relevance to Auckland are probably limited to ammonia, nitrate, Cu, Zn, Pb and petroleum products (total petroleum hydrocarbons (TPHs), polycyclic aromatic hydrocarbons (PAHs)), with the latter largely associated with stormwater discharges. Criteria for these contaminants are described in this chapter. Toxic algae are discussed in the previous chapter. Many other potentially toxic contaminants are listed in criteria tables such as the ANZECC guidelines; to date none of these have been shown to be an issue for Auckland. Should other dissolved toxic contaminants (say associated with point source discharges) become an issue in Auckland, then reference can be made to the comprehensive list of toxicants in the ANZECC (2000) guidelines under a catch-all guideline category. No guidelines exist for the management of other contaminants of lower toxicity, or which have currently unrecognised biochemical or ecosystem effects. These are collectively termed Chemicals of Emerging Potential Concern (CEPC) or simply emerging contaminants (ECs). They include pharmaceuticals, animal remedies, plasticisers, petroleum constituents, surfactants, and cleaners. A recent study of 23 estuarine sites around Auckland identified residues of ECs at various sites, with 21 pharmaceutical compounds present at one or more sites (Stewart et al. 2014). In the following, we summarise Schedule 3 of the RMA and the ANZECC Guideline approach to toxicants because these are common to all the toxicants (ammonia, nitrate, heavy metals, toxic organics) in this chapter. Schedule 3 RMA Schedule 3 of the RMA has explicit narrative standards for toxic contaminants for Class AE Waters (Table 5-1) similar standards are implicit in Class NS and C Waters. Technical aspects of integrating water quality science in freshwater and coastal environments 53

64 Table 5-1 Standards for Toxic Contaminants for Water Quality Classes from Schedule 3 RMA. Class Purpose Criteria AE Aquatic ecosystem The following shall not be allowed if they have an adverse effect on aquatic life: (c) any discharge of a contaminant into water F FS SG Fisheries Fish spawning Gathering/Cultivating shellfish CR Contact Recreation - WS Water supply The water shall not be tainted or contaminated so as to make it unpalatable or unsuitable for consumption by humans after treatment (equivalent to coagulation, filtration, and disinfection), or unsuitable for irrigation. I Irrigation (see above) IA Industrial abstraction - NS Natural state The natural quality of the water shall not be altered A Aesthetic - C Cultural The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values ANZECC Guidelines The ANZECC (2000) guidelines provide comprehensive guidance for toxicity assessment. They use a decision tree approach for assessing toxicity. As with all their guidelines, they list trigger values or they propose that users develop sitespecific guideline values. Two responses are possible if triggers are exceeded: 1) Incorporation of additional information or further site-specific investigation to determine whether the chemical is posing a real risk to the environment. 2) Accept the trigger value without change as a guideline applying to the site and initiate an investigation. Technical aspects of integrating water quality science in freshwater and coastal environments 54

65 Investigations as to whether the chemical is posing a real risk or not usually follow application of relevant decision trees. This approach is relatively complex, and not suitable to simple pass/fail concentration values. As outlined in Section above the first step is choosing the level of protection, and that depends on the ecosystem condition. ANZECC (2000) recognised three types of ecosystem conditions: 1) high conservation/ecological value 2) slightly to moderately disturbed ecosystems 3) highly disturbed ecosystems. Appropriate levels of protection must be selected, often in consultation with stakeholders, and are typically either: 1) 99%, 2) 95%, 3) 90% or 80% across these conditions (see ANZECC (2000) page ). These levels of protection can be directly related to summaries of toxicity information. 5.2 Ammonia Overview Ammonia is a basic industrial chemical, a product of organic matter decomposition, a soil nutrient, and a common constituent of human and animal wastes. It commonly occurs in point source discharges, catchment runoff and receiving waters in the Auckland region, but usually at low, non-toxic concentrations. The main concerns are associated with elevated levels in human and animal wastes and in enriched sediments. Ammonia occurs as two forms that are in equilibrium in water: unionised ammonia (NH 3 ) and ionised ammonia (NH 4 + ); and its toxicity is mainly associated with the unionised form. Its toxicity is well characterised. The toxicity of a solution containing ammonia depends on the equilibrium between the two forms, which in turn depends on the ph, temperature and salinity of the water body Use/applicability/importance Ammonia is relevant in freshwaters receiving wastewater discharges that contain high concentrations of ammonia. All guidelines and the NOF standards require consideration of receiving water ph as part of the compliance assessment process Critique/review of existing and proposed approaches to nutrient enrichment management/guidelines The various available guidelines are summarised in Appendix B and described below. Technical aspects of integrating water quality science in freshwater and coastal environments 55

66 Schedule 3 RMA Schedule 3 Narrative Standards for toxicants in general are described above in Section 5.1. Ecosystem health ANZECC Guidelines The ANZECC (2000) guidelines for waters are currently higher than the recently revised US EPA guidelines (US EPA 2013) and the NOF standards (MfE 2014a). They are likely to change with the current revision of the ANZECC guidelines. The revised ANZECC (2000) guidelines will also have unique guidelines for ammonia in marine sediments (i.e., in the sediment pore water), but no guidelines have been derived for freshwater sediments. Table 5-2 lists values for the ANZECC (2000) trigger values for freshwater at ph 8.0. The guidelines can be consulted for ammonia levels at other temperature, ph and salinity situations. Table 5-2 ANZECC (2000) trigger values for Total Ammoniacal-nitrogen (TAN) in freshwater at ph 8. Level of protection 99% 95% 90% 80% 320 µg/l 900 µg/l 1430 µg/l 2300 µg/l The Environmental Response Criteria (ARC 2002) recommended using ANZECC (2000) guidelines. Ecosystem health NPS-FM The NPS-FM lists ammonia as a compulsory attribute for ecosystem health in rivers and lakes. NOF bands for toxicants are derived on the same basis as the ANZECC guidelines to provide a range of thresholds (i.e., bands) for differing levels of protection from chronic effects on aquatic species. The NOF standards for ammonia are comparable to the proposed updated ANZECC guidelines and are applicable to rivers and lakes (Table 5-3). The NOF guidelines are lower than the previous ANZECC (2000) guidelines following inclusion of new data regarding the protection of freshwater mussels (Clearwater et al. 2014), which were included in recently revised US EPA ammonia guidelines (US EPA 2013). Technical aspects of integrating water quality science in freshwater and coastal environments 56

67 Table 5-3 Numeric and narrative attribute states for the attribute ammonia for ecosystem health in rivers and lakes at ph 8 and 20 C. Compliance with numeric attribute states should be undertaken after ph adjustment (MfE 2014a). Attribute state Numeric Attribute State Narrative Attribute State Annual median (mg/l) Annual maximum (mg/l) A % species protection level: no observed effects on any species tested B >0.03 and >0.05 and 95% species protection level. Starts impacting occasionally on the 5% most sensitive species C >0.24 and >0.40 and 80% species protection level: Starts impacting regularly on the 20% most sensitive species (reduced survival of most sensitive species) National Bottom Line D >1.3 >2.20 Starts approaching acute impact level (i.e., risk of death) for sensitive species ANZECC physico-chemical trigger values The ANZECC (2000) physico-chemical trigger values are summarised in Appendix B and discussed in section These numeric values provide benchmark concentrations and do not relate to thresholds for adverse effects. They would be best replaced by data from local reference sites if the change from background approach were to be used for Auckland streams and rivers. Aquaculture ANZECC (2000) recommends guideline values for cold freshwater of <0.025 mg NH 4 -N/L at ph >8.0 and 0.0 mg NH 4 -N/L at ph <8.0 (Table ). We note that the guideline value for ph >8 is markedly lower than the ANZECC trigger value for ecological protection (0.9 mg NH 4 -N/L). The 0.0 value is probably an error because the toxicity of ammonia decreases as the water ph decreases. Technical aspects of integrating water quality science in freshwater and coastal environments 57

68 Human recreation The ANZECC (2000) guidelines provide a human health primary contact guideline value of 10 µg NH 4 -N/L for freshwaters (ANZECC 2000, Table 5.2.3). No derivation or justification is provided to support this particularly low guideline value in the Guidelines for recreational water quality and aesthetics section (Chapter 5). Accordingly we do not recommend its use. The aesthetic guideline (below) may be applied to some recreational waters. Drinking water There are no drinking water guidelines for ammonia (MOH 2008). Elevated ammonia concentrations may cause problems in water supplies when treated with chlorine because of the formation of chloramines, which are an odour problem for consumers (MOH 2013). Aesthetics The guideline for ammonia for aesthetic determinants is 1.5 mg NH 4 -N/L (MOH 2008). This is based on the odour threshold for ammonia in alkaline conditions (MOH 2008, Table 2.5). Stockwater and irrigation No stockwater or irrigation guidelines are provided for ammonia in ANZECC (2000). We would not anticipate any issues for these purposes at expected surface water or groundwater ammonia concentrations. Overall, current guideline values and any revisions of ANZECC and NOF Bands are considered appropriate Relevance/suitability for Auckland Ammoniacal-N is currently measured monthly at 34 river and stream sites for SoE monitoring, with a requirement of value to be less than 0.06 mg N/L for this parameter as one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). The ammoniacal-n threshold was exceeded at 47% of the sites. The site monitoring data cannot readily be compared with the NOF standards because of the requirement to compare the attribute classes with ph-adjusted ammoniacal-n concentrations (MfE 2014a). Ammonia toxicity is an important consideration with wastewater and industrial discharges to streams and rivers. Diffuse source pollution by ammonia is not expected to be a problem in terms of streams breaching the bottom-line, but may contribute to a lower attribute state in some situations. Technical aspects of integrating water quality science in freshwater and coastal environments 58

69 5.2.5 Recommendations We recommend that the NOF Numeric Attribute States for different levels of protection are used for the value Aquatic Health (Table 5-2), which will require measurement of ph. Temperature and ph dependent guidelines are likely to be incorporated in the revised ANZECC guidelines. Accordingly, more complex monitoring (including ph and temperature), will be required. 5.3 Nitrate Overview Nitrate (a soil nutrient), is a product of organic matter decomposition, including human and animal wastes. It commonly occurs in diffuse runoff, groundwater, catchment runoff and receiving waters in the Auckland region, but usually at low, non-toxic concentrations. The main concerns are associated with leaching of nitrate from pasture soils to groundwater and stream receiving waters Use/applicability/importance Nitrate is relevant in freshwaters receiving groundwater discharges that contain high concentrations of nitrate Critique/review of existing and proposed approaches to nitrate toxicity guidelines Schedule 3 RMA Schedule 3 Narrative Standards for toxicants in general are described above in Section 5.1. Ecosystem Health - ANZECC Guidelines The ANZECC (2000) guidelines for freshwaters included nitrate toxicity, however, this was identified as having errors in its derivation (Hickey 2002). The nitrate guideline were recently updated to include new data (Hickey 2013). This updated derivation forms the basis of the NOF standards (MfE 2014a), and will be included in the current ANZECC guideline revisions. Ecosystem health NPS-FM The NPS-FM lists nitrate as an attribute for ecosystem health in rivers, with assessments based on annual median and annual 95 th percentile values. Nitrate was not included as a NOF standard for lakes because the lake median total nitrogen concentration standard was considered to be so low that it adequately covered any potential toxicity-related effects. The NOF Bands are shown in Table 5-4. Technical aspects of integrating water quality science in freshwater and coastal environments 59

70 Table 5-4 Numeric and narrative attribute states for the attribute nitrate for ecosystem health in rivers. (MfE 2014a). Attribute state Numeric Attribute State mg/l Annual median Annual 95 th percentile Narrative Attribute State A High conservation status system. Unlikely to be effects even on sensitive species B >1.0 and 2.4 >1.5 and 3.5 Some growth effects on up to 5% of species C >2.4 and 6.9 >3.5 and 9.8 Growth effects on up to 20% of species (mainly sensitive species such as fish). No acute effects National Bottom Line D >6.9 >9.8 Impact on growth of multiple species, and starts approaching acute impact level (i.e., risk of death) for sensitive species at higher concentrations (>20 mg/l) ANZECC physico-chemical trigger values The ANZECC (2000) physical-chemical trigger values for nitrate-n provide values of 167 µg NO 3 -N/L in upland and 444 µg NO 3 -N/L in lowland rivers (Appendix B, Table B2). These values do not represent any basis for the establishment of adverse ecosystem effects. As such, they should not be used in a regulatory context. Aquaculture The ANZECC (2000) guideline for freshwater aquaculture is 50 mg NO 3 /L (11.3 mg NO 3 -N/L) (Table ). This value is comparable with the drinking water guideline but higher than the ecological guidelines for sensitive species. Drinking water The drinking water guideline for nitrate is 50 mg NO 3 /L (11.3 mg NO 3 -N/L) for shortterm exposure (Table 2.2) (MOH 2008). Ministry of Health state that: The short-term exposure MAVs for nitrate and nitrite have been established to protect against methaemoglobinaemia in bottle-fed infants. The drinking water guideline is termed a Maximum Acceptable Value (MAV) and is based on a 95 th percentile measurement. High nitrate concentrations occur in drinking-water sources in a number of areas in New Zealand. A number of possible sources exist, all related to human land use activities such as: fertiliser application; disposal of wastewater from dairy factory Technical aspects of integrating water quality science in freshwater and coastal environments 60

71 operations; high grazing densities of dairy stock. It can also be found at high concentrations on a localised scale due to on-site waste disposal systems (e.g., septic tanks) (MOH 2013). There are also guidelines for nitrite concentrations for drinking water protection (MOH 2008). Human recreation The ANZECC (2000) guidelines provide a human health primary contact guideline value of 10.0 mg NO 3 -N/L and 1.0 mg NO 2 -N/L for freshwaters (ANZECC 2000, Table 5.2.3). This nitrate guideline value is similar to the drinking water guideline. Stockwater and irrigation There are no stockwater or irrigation guidelines for nitrate in ANZECC (2000). We would not anticipate any issues regarding use for these purposes at expected surface water or groundwater nitrate concentrations Relevance/suitability for Auckland Total oxidised nitrogen (nitrate + nitrite) is currently measured monthly at 34 river and stream sites for SoE monitoring, but this parameter is not one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). Only one of the monitored sites (Whangamaire, median 13.5 mg N/L, maximum 16.0 mg N/L) exceeded the minimum acceptable national bottom line for nitrate toxicity in rivers (6.9 mg nitrate-n/l) in the NOF standards (MfE 2014a). Many of the other sites monitored would exceed the lower NOF attribute bands for nitrate. Nitrate concentrations in the south Auckland freshwater systems in Franklin are particularly elevated and are above relevant environmental and human health guidelines and have increased over time (Auckland Council 2014a). Nitrate toxicity is an important consideration with wastewater discharges and in highly developed pasture systems, especially intensive dairy farming. It can also be found in small streams draining rural settlements which are serviced by septic tanks Recommendations We recommend that the NOF Numeric Attribute State for nitrate for different levels of protection are used for the values ecosystem health in streams receiving waste water discharges and impacted by intensive agriculture and for the value drinking water in groundwater (Table 5-4). Existing measurement protocols remain appropriate for future monitoring requirements. Technical aspects of integrating water quality science in freshwater and coastal environments 61

72 5.4 Heavy metals: copper (Cu), lead (Pb) and zinc (Zn) Overview Cu, Pb and Zn are well-known contaminants in urban runoff that can be toxic in water at relatively low concentrations. They have been extensively studied, so their toxicity is well understood. However, for any given concentration, toxicity can vary widely across different receiving waters depending on the types of animals present and the chemical characteristics of the water Use/applicability/importance Copper is a common contaminant in Auckland in stormwater and the major source in urban runoff is vehicle brake linings, which have been estimated to contribute as much as 75 per cent of the copper input to runoff from Auckland s CBD (Kennedy et al. 2008). Its use in existing and historical horticultural areas may contribute to rural and urban runoff. Lead is a common contaminant in Auckland in stormwater, chiefly from its historical use as an additive in petrol. Lead is still being discharged from urban areas despite having been removed from petrol nearly two decades ago. Present day sources include buildings (historical use of lead-based paints, lead flashing/plumbing) and the mobilisation of Pb that had accumulated in soils near buildings and roads subject to input from paint and petrol residues. Zinc is a common contaminant in Auckland in stormwater and rural runoff, because of structures (galvanised iron, fencing), paints and paint removal (e.g., on steel structures), point sources and animal remedies (e.g., use as facial eczema treatment for livestock in pasture areas) Critique/review of existing and proposed approaches to nutrient enrichment management/guidelines Schedule 3 RMA Schedule 3 Narrative Standards for toxicants in general are described above in Section 5.1. Ecosystem Health - ANZECC guidelines The current ANZECC (2000) guideline trigger values are under review and are likely to be revised slightly. The 2000 trigger values are listed in Table 5-5 in relation to ANZECC levels of protection and provided in Appendix B (Table B2) together with ecosystem marine guidelines and other freshwater guidelines. The ANZECC (2000) approach was described in Section Technical aspects of integrating water quality science in freshwater and coastal environments 62

73 Table 5-5 ANZECC (2000) trigger values (chronic) and US EPA (2006) criterion maximum concentration (CMC, acute) values for Cu, Pb and Zn in freshwater waters. Standard hardness for guidelines of 30 mg CaCO 3 /L. ANZECC (chronic): Level of protection (µg/l) US EPA (acute) (µg/l) 99% 95% 90% 80% 95% Cu Pb Zn The trigger values for Cu are particularly stringent and may often be breached for higher levels of protection in urban streams and may sometimes be exceeded in rural streams. The ANZECC (2000) trigger values (and eventually the revised values) are highly appropriate for filterable Zn, Cu and Pb concentrations in Auckland waters. It is highly unlikely that Pb concentrations will exceed trigger values because the fraction of soluble and therefore potentially bioavailable Pb is well below trigger values. Background concentrations for Cu and Zn are not well understood currently. Improved information is required in order to manage these metals robustly (ANZECC (2000) page ), because trigger levels are close to background. There is information available from past and present studies in Auckland (reviewed in Mills et al. 2008; Williamson et al. 2009). Ecosystem Health US EPA Guidelines If management of short-term pulses of toxicants to surface waters, such as might occur in urban stormwater, is desired, it may be necessary to specify maximum concentrations. These are not available in the ANZECC (2000) guidelines, but it has been proposed that the updated ANZECC guidelines will provide maximum (i.e., acute values). Until these are available, we recommend the US EPA Ambient Water Criteria - Criteria Maximum Concentration (CMC) is used (US EPA 2006). These criteria should be assessed following the tiered assessment protocol for metal speciation as recommended by ANZECC (2000; Figure 3.4.2), which distinguishes the dissolved fraction, makes water hardness adjustment and takes into account other bioavailability assessments. The CMC is an estimate of the highest concentration of a material in surface water to which an aquatic community can be exposed briefly without an unacceptable effect (= acute concentration). [Note that the Criterion Continuous Concentration (CCC) is an estimate of the highest concentration of a material in surface water to which an aquatic community can be exposed indefinitely without an unacceptable effect (= Technical aspects of integrating water quality science in freshwater and coastal environments 63

74 chronic concentration). The CMC and CCC are just two of the six parts of an aquatic life criterion in the USA; the other four parts are the acute averaging period, chronic averaging period, acute frequency of allowed exceedance, and chronic frequency of allowed exceedance. ( Aquaculture The ANZECC (2000) recommended guidelines for freshwater aquaculture are: Cu <0.005 mg/l (hardness-dependent, Table ); Pb < mg/l (hardnessdependent, Table ); Zn <0.005 mg/l (Table ). Information provided in the summary tables for each of these metals provides guidelines specific to fish species and general aquatic organism protection. Drinking water The drinking water guidelines are: Cu, 2 mg/l; Pb, 0.01 mg/l and Zn, no consumption guideline (Table 2.2) in MOH (2008). The Drinking Water Guideline MAVs are based on a 95 th percentile measurement. Specific guidance is provided by MOH (2013) in relation to the use of copper to control algae and cyanobacteria in drinking water reservoirs. Human recreation The ANZECC (2000) guidelines provide a human health primary contact guideline value of: Cu, 1.0 mg/l; Pb, mg/l; and Zn, 5.0 mg/l (ANZECC 2000, Table 5.2.3). These metal guideline values for recreation are not comparable with the drinking water guideline and the basis for their derivation is not known. Aesthetics The aesthetic guidelines are: Cu, 1 mg/l; Pb, no guideline; Zn, 1.5 mg/l (Table 2.5) in MOH (2008). The Cu is based on staining of laundry and sanitary ware, and Zn on taste threshold. Stockwater and irrigation The ANZECC (2000) stockwater guidelines are: Cu, 0.4 mg/l (sheep), 1 mg/l (cattle), 5 mg/l (pigs), 5 mg/l (poultry); Pb, 0.1 mg/l; Zn, 20 mg/l. (Table 4.3.2) in ANZECC (2000). The ANZECC (2000) irrigation water guidelines are provided as long-term trigger values (LTV up to 100 yrs) and short-term trigger values (STV up to 20 yrs): Cu, 0.2 mg/l LTV, 5 mg/l STV; Pb, 2 mg/l LTV, 5 mg/l - STV; Zn, 2 mg/l LTV, 5 mg/l LTV (Table ) in ANZECC (2000). Technical aspects of integrating water quality science in freshwater and coastal environments 64

75 Ecosystem Health - General aquatic toxicity testing Another approach, particularly for point source discharges, is to use toxicity testing. This is a well-developed approach and is routinely available in New Zealand at a number of specialist laboratories. Toxicity testing includes WETT (Whole Effluent Toxicity Testing) and DTA (direct toxicity assessment ANZECC (2000)). A range of well-developed standard techniques, which involve tests of aquatic animals in laboratories, could be used to develop toxicity guidelines. The most obvious application is for point sources that discharge multiple toxicants (e.g., the tests would need to show that the effluent is not toxic to appropriate test organisms after reasonable mixing). Expert opinion from a qualified ecotoxicologist would be required to establish site-specific quality guidelines for point discharges. Ecosystem Health - Developing a Robust Copper Criterion the Biotic Ligand Model A promising new approach, which has been successfully applied for Cu in freshwater, makes use of the Biotic Ligand Model (BLM). These approaches are described below. The BLM computer model uses 10 water chemistry parameters to calculate a freshwater copper criterion. The BLM is used extensively in the USA and forms the basis of US EPA s 2007 national recommended 304(a) freshwater criterion for copper (US EPA 2007) 4. A suitable criterion value could be developed in Auckland using this procedure. It is possible that the technique will be extended to include Zn (van Genderen et al. 2009) and other metals (e.g., Ni). In general, the BLM allows regulators and dischargers to account for the effect of additional water chemistry parameters (e.g., DOC, ph, major ions, and alkalinity) on the toxicity of metals to aquatic organisms. Using the BLM provides more accurate WQC without the expense or time required for deriving a water effect ratio (WER). The ideas behind the BLM are not new. Similar ideas were proposed nearly 30 years ago (such as Pagenkopf s Gill Surface Interaction Model, and the Free Ion Activity Model). A number of water quality variables can affect metal toxicity, particularly Natural Organic Matter (NOM), and ph, which have a strong effect on copper toxicity. Other variables including hardness cations, alkalinity, and sodium may also play a role. Failure to consider these effects may make a WQC overprotective or under protective for a large number of sites where permits for metals discharges are 4 cfm Technical aspects of integrating water quality science in freshwater and coastal environments 65

76 needed. The BLM can be used to consider these effects when developing copper criteria. It predicts acute freshwater WQC using an approach similar to that used when predicting organism toxicity. Chronic WQC derived are then derived from an acute criterion using the Acute/Chronic Ratio (ACR). The BLM requires a description of water chemistry parameters able to influence metal toxicity. These parameters include: ph; DOC (a convenient measure of NOM); and major ion concentrations. Major ions also have specific effects on copper toxicity including: ionic strength, which affects speciation calcium, magnesium, and sodium (which can all reduce copper toxicity) either alkalinity or DOC (used by the BLM to estimate copper-bicarbonate complexation). Copper toxicity in freshwater fish occurs due to disruptions of ion regulation in gill membranes. Similar mechanisms have been demonstrated for other aquatic organisms. Anything that might affect how copper interacts with gill membranes (such as the presence of calcium in the water) may also influence copper toxicity Relevance/suitability for Auckland Heavy metals (total and dissolved copper, zinc and lead) concentrations are currently measured monthly at 24 river and stream sites for SoE monitoring, but these parameters are not included in the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). The dissolved metal concentrations from these sites may be compared with the ANZECC (2000) trigger value for a nominal 80% species protection, in order to provide an indication of the likely national bottom line threshold if NOF standards were to be introduced. Comparison with the ANZECC Technical aspects of integrating water quality science in freshwater and coastal environments 66

77 80% protection values indicate: copper, 42% of the sites exceed the guideline (2.5 µg Cu/L); zinc, 38% of the sites exceed the guideline (31 µg Zn/L); and lead, none of the sites exceed the guideline (9.4 µg Pb/L). High zinc loads may occur from both urban stormwater and possibly in rural catchments as a result of the use of zinc dosing of livestock for facial eczema management, resulting in elevated stream concentrations. Data on water quality monitoring, including heavy metal concentrations, have been summarised for a range of aquifer types from a wide variety of locations sampled from the period (ARC 2007). The authors state that an assessment of suitability for drinking water supply should be based on the NZ drinking water guidelines and the ANZECC (2000) guidelines were used to assess the environmental health of the groundwater and any potential risk to the environment. No analyses of the summarised data presented in that report were undertaken as part of this study. Cadmium, added as a contaminant in phosphatic fertilisers to pasture soils of the Mahurangi catchment is mobile through both leaching from the acidic soils and erosion, and has been found to significantly accumulate in oysters (Butler et al. 1996). These data indicate that cadmium may also be a contaminant of potential concern for adverse effects on both freshwater and marine ecosystems Recommendations Cu and Zn We recommend that trigger levels for different levels of protection for dissolved (i.e., filterable) Cu and Zn are adopted from the revised ANZECC guidelines (Table 5-5). The current ANZECC (2000) guideline trigger values are under review and small changes are likely. A decision would need to be made whether to accept trigger values as standards, or promote the approach which investigates whether any exceedances represent a real risk to aquatic ecosystems. If the former is used, then the numerical objectives would be the trigger values listed in Table 5-5. As described above, this may be challenging to meet in urban and rural streams. We recommend the latter approach using the ANZECC protocols: a well-designed and executed study should provide numerical objectives that are applicable across the region. Monitoring will require adequate detection limits (preferably at least 1/10 of any standard or numerical objective). It is possible that the more robust Biotic Ligand Model (BLM) currently used in the USA to determine Cu guidelines for freshwater, could be adapted for Auckland. This approach may also extend to Zn guidelines in the future. Auckland Council will need to keep abreast with developments of this model. Technical aspects of integrating water quality science in freshwater and coastal environments 67

78 Heavy metals are elevated in urban streams during base and storm flows. Their management is quite challenging. Urban streams will have relatively high concentrations of Zn and Cu (Mills et al. 2008), but management would probably opt for a low level of protection (which reflect the high level of stressors), otherwise they would be very difficult to manage/fix. If treatment devices are applied, then each type of treatment device is able to treat a different range of effluent concentrations, with high uncertainty regarding performance values; and different flow and efficacy of treatment in response to storms. The requirement to consider low flow, storm flow and the influence of treatment requires careful consideration of the statistic that would be used to specify numeric attribute values. The urban stream classification would also need to be considered. The complexity arising from these factors would make detailed critical review mandatory. If the urban stormwater receiving waters have a high level of ecosystem protection (i.e., equivalent to NOF A, B) then improved treatment (e.g., treatment trains) would probably need to be provided to achieve the chronic band level. It seems highly unlikely that widespread treatment would be implemented because of the high cost. Other metal and metalloid toxicants in water Pb is unlikely to be toxic in the water column under most conditions because the concentration of the dissolved fraction is usually very low, well below trigger values. On the basis of existing information regarding low concentrations, we recommend that plans do not specifically include trigger levels for lead, but that it is included in a catch-all clause. Other metal and metalloid toxicants have not been identified at potentially toxic concentrations in surface waters around Auckland, except for possibly cadmium. As a result, requirements for their management will probably be infrequent and usually associated with contaminated sites or industrial point sources. We recommend that all plans refer to the possibility of using ANZECC trigger levels in a catch-all clause for any metals, metalloids and organics identified in the future as representing a threat to aquatic ecosystems and therefore requiring management. This approach is limited to those metal, metalloid and organic toxicants listed in ANZECC, which does not cover many of the emerging contaminants. 5.5 Organics Overview A large range of potentially toxic organic compounds are used in industry, as pesticides, as household products, as by-products of chlorination of water supplies and wastewater, pharmaceuticals, in petroleum products, as leachates from other materials and as by-products of combustion. Most are not expected to be Technical aspects of integrating water quality science in freshwater and coastal environments 68

79 encountered around Auckland, and especially not in the dissolved phase. They are sometimes looked for in sediment screening analyses, and some are occasionally detected (Depree et al. 2007) Use/applicability/importance The chemicals currently in use are not known to cause problems around Auckland and are not expected to cause problems. They are monitored only in specific situations Critique/review of existing and proposed approaches to organic toxicants management/guidelines Schedule 3 RMA Schedule 3 Narrative Standards for toxicants in general are described above in Section 5.1. ANZECC Guidelines ANZECC (2000) list trigger values for a number of organic contaminants used in industry and agriculture. These include solvents, chemicals used in manufacturing, plasticizers, pesticides, and surfactants (see ANZECC (2000) Table 3.4.1). Toxicity assessment For specific discharges of industrial chemicals, a toxicity assessment approach may be better than application of guidelines. This is because there may be multiple toxicants (and hence changes in toxicity due to toxicant interactions) and/or a complex chemical matrix which affects toxicant toxicity Relevance/suitability for Auckland The current SoE monitoring programme does not include any organic contaminants (Lockie et al. 2013). Impacts associated with chemical use in Auckland are expected to be rare. Concentrations of some of the more common organic contaminants e.g., polycyclic aromatic hydrocarbons (PAH), total petroleum hydrocarbons (TPH) are relatively low (Mills and Williamson 2008) Recommendations The ANZECC (2000) guidelines could be used where these chemicals are expected to be a problem. For specific discharges of industrial chemicals, a toxicity assessment may be better than using guidelines. Technical aspects of integrating water quality science in freshwater and coastal environments 69

80 6 Human Health 6.1 Human health risks in the aquatic environment Risk associated with primary recreation is largely determined by health risks, which in turn are determined by the risk of disease and by physical hazards. The importance of water clarity has been briefly discussed elsewhere (see section 3.5, Clarity). The quality of water in which contact recreation activities (swimming, skiing, paddling, kayaking, shellfish gathering and consumption) occur needs to be such that neither accidental ingestion of small quantities of the water nor consumption of shellfish results in illness. When involved with these activities there is a reasonable risk that water will be swallowed, inhaled, or come in contact with ears, nasal passages, mucous membranes or cuts in the skin, allowing pathogens to enter the body (MfE/MoH 2003). The risk of catching a water-borne disease is determined by many factors, but of primary interest is the concentration of pathogenic microorganisms in the water column. Water contaminated by human or animal excreta may contain a range of pathogenic (disease-causing) micro-organisms, such as viruses, bacteria and protozoa. 6.2 Use/applicability/importance Faecal coliforms and E. coli are used to assess the risk to human health in contact recreation, and these are key indicators of freshwater water quality. Stormwater runoff invariably contains high levels of indicator bacteria irrespective of land use, although developed land will have higher concentrations than undeveloped land. Sources of faecal contaminants in urban stormwater include birds, dogs, cats, rats (either by direct input to surface waters, or of indicator bacteria associated with soils and sediments), leaky sewerage, and pump overflows. Studies in New Zealand have shown that farmed livestock, along with birds, are a significant source of microbial contaminants entering water bodies (McBride 2002). Pathways of water contamination are varied and complex, including direct deposition (e.g., from stock in waterways), surface runoff, and movement through the soil profile. The relative importance of these pathways is influenced by a range of factors: e.g., soil type, slope, soil moisture content, rainfall, and farm management practices. While stock spend relatively little time in water bodies while grazing, they tend to defecate disproportionately more in those water bodies, with significant impact on microbial loadings. Soils that are naturally poorly drained are often associated with high by-pass flow of microbes via soil cracks or worm channels, whereas naturally freer draining soils may provide greater attenuation of microbes as they pass through Technical aspects of integrating water quality science in freshwater and coastal environments 70

81 the soil profile. Significant microbial flows may also pass through the drainage channels of artificially drained soils. 6.3 Critique/review of existing and proposed approaches to microbial contamination management/guidelines A summary of existing numerical guidelines in available in Appendix Table B2. Schedule 3 RMA Schedule 3 of the RMA specifies a narrative microbiological standard for SG and CR waters, which are implicit in Class C Waters (Table 6-1). Table 6-1 Standards for Microbiological Quality for Water Quality Classes from Schedule 3 RMA. Class Purpose Criteria AE Aquatic Ecosystem - F Fisheries - FS Fish Spawning - SG Gathering/Cultivating shellfish Aquatic organisms shall not be rendered unsuitable for human consumption by the presence of contaminants CR Contact Recreation The water shall not be rendered unsuitable for bathing by the presence of contaminants WS I Water Supply Irrigation IA Industrial Abstraction - NS Natural State - A Aesthetic C Cultural The quality of the water shall not be altered in those characteristics which have a direct bearing upon the specified cultural or spiritual values MFE Guidelines Microbiological guidelines for recreation and shellfish gathering in marine and fresh waters are provided in MFE These guidelines present a protocol for determining (and grading) the suitability of waters for recreational use. There are surveillance, alert, action levels as described in Section It is difficult and impractical to measure the level of pathogens in the water directly. Instead, levels of indicator bacteria are measured. If a robust monitoring approach is followed, these provide an indication of the likely pathogenicity of the water. This Technical aspects of integrating water quality science in freshwater and coastal environments 71

82 strategy was comprehensively reconfirmed by a recent study (Till et al. 2008) 5. Numerical guidelines for shellfish tissue, water quality for shellfish gathering and water contact are summarised below. For freshwaters, the faecal indicator micro-organism used is Escherichia coli (E. coli) which is found in the gut of humans, farm animals and wildlife, and is a convenient indicator of faecal pollution and associated health risks. Some diseases, zoonoses, can be caused by microorganisms shed by animals. This can occur by direct contact with animals and their wastes, or more commonly, through contaminated food and water. High E. coli concentrations in rivers and lakes, whether of human or animal origin, indicate a risk to public health. There are two components for grading freshwater recreational sites: (1) the Sanitary Inspection Category, which measures the susceptibility of a water body to faecal contamination, (2) use of historical microbiological results to generate a Microbiological Assessment Category (Section 6.2.3). This provides a measurement of water quality over time. These are combined to produce a Beach Grade. The microbiological guidelines and grading system are widely used throughout New Zealand, including Auckland. Although wastewater treatment processes often effectively reduce microbial indicators, they are less effective at removing pathogens such as viruses. The result may be an altered pathogen-to-indicator ratio relative to that of untreated waste. This means that if a site is subject to discharge from a wastewater treatment plant, pathogens may still be present even when indicator levels are very low (MoH/MfE 2003). In these circumstances it is better to conduct a Quantitative Microbial Risk Assessment (QMRA), which is described below. The MfE Guidelines used QMRA to develop the numerical values. Water Quality for Shellfish Gathering: MFE (2003) Median FC over shellfish gathering season <14 MPN per 100 ml No more than 10% of samples >43 MPN per 100 ml Freshwater (and Marine in special circumstances) Water Quality for Contact Recreation The indicator organism is E. coli, and water quality limits based on 95%iles with a requirement to collect a minimum of 20 samples over the bathing season (Hazen method). 5 However, national guidelines recommend that pathogen assays be carried out in situations where human exposure takes place in close proximity to discharges of treated sewage. Technical aspects of integrating water quality science in freshwater and coastal environments 72

83 Microbiological Assessment Category (Hazen 95%iles, per 100 ml): A: <130 B: C: D: >550 Green/acceptable surveillance mode: No single sample >260. Continue weekly sampling. Amber/Alert mode: single sample >260. Increase to daily sampling. Sanitary survey. Red/Action mode: single sample >550. Daily sampling. Sanitary survey. Warning signs NPS-FM The NPS-FM lists E. coli as a compulsory attribute for human health for secondary contact recreation in rivers and lakes. Secondary contact means people s contact with fresh water likely to result in occasional immersion and includes wading or boating (except boating where there is high likelihood of immersion) (MfE 2014a). The provision of numeric thresholds for secondary contact recreation in the NOF (none existed previously), requires a decision as to whether or not it is appropriate to manage some rivers and streams in the region for secondary contact recreation only. The NOF Bands are shown in Table 6-2. The bands differ significantly from the Microbiological Assessment Categories in the Freshwater (and Marine in special circumstances) Water Quality for Contact Recreation Guidelines (MFE 2003) described above. Although the NOF attribute states differ from the current MfE (2003) guidelines in a number of ways, they share use of risk data to determine human health risks associated with full immersion (primary recreation). Differences include: Although the Microbiological Assessment Category (MAC) has four grades (A, B, C, D (Section 6.2.3)), and the NOF bands have four categories (A, B, C, D), the numeric thresholds of these classification systems are not related The NOF numeric attribute bands includes risks associated with both secondary and primary recreation (Table 6-2). The NOF bands for secondary contact are mandatory, while the bands for primary contact are optional (Table 6-2). The secondary contact assessment would generally be based on the median data, whereas primary contact would be based on the 95 th percentile values. A draft guidance document for implementation of the NOF Technical aspects of integrating water quality science in freshwater and coastal environments 73

84 standards has been released (MfE 2014b), however, no technical details for monitoring and assessment have been released to date (as at 15 December 2014). When available, these will provide the guidance needed for frequency of sampling, averaging periods for data and spatial assessment of monitoring sites. Table 6-2 NOF faecal indicator thresholds for secondary contact (MfE 2014). Attribute Numeric Sampling Narrative Attribute State State Attribute statistic State (E.coli /100 ml) A 260 Annual median People are exposed to a very low risk of infection (<0.1% risk) from contact with water during activities with occasional immersion and some ingestion (such as wading and boating) 95 th %tile People are exposed to a low risk of infection (<1% risk) when undertaking activities likely to involve full immersion B >260 and 540 Annual median People are exposed to a low risk of infection (<1% risk) from contact with water during activities with occasional immersion and some ingestion (such as wading and boating) 95 th %tile People are exposed to a moderate risk of infection (<5% risk) when undertaking activities likely to involve full immersion. 540 / 100 ml is the minimum acceptable state for activities likely to involve full immersion. C >540 and 1000 National bottom line Annual median 1000 Annual median D >1000 Annual median People are exposed to a moderate risk of infection (<5% risk) from contact with water during activities with occasional immersion and some ingestion (such as wading and boating). People are exposed to a high risk of infection (>5% risk) from contact with water during activities likely to involve full immersion. People are exposed to a high risk of infection >5% risk) from contact with water during activities with occasional immersion and some ingestion (such as wading and boating) Quantitative Microbiological Risk Assessment QMRA uses the best measurements of microbes behaviour to identify where they can become a danger and estimate the risk (including the uncertainty in the risk) that they pose to human health 4. QMRA has been used in New Zealand to characterise the risk of treated sewage discharges to human health at a number of freshwater and marine locations including the following Auckland sites: Beachlands, Waiwera, Warkworth (Mahurangi Harbour) and Helensville (Kaipara Harbour) (McBride 2008a; McBride 2008b; Palliser 2009a; Stott et al. 2004; Stott et al. 2008). Technical aspects of integrating water quality science in freshwater and coastal environments 74

85 QMRA has four stages 6 : Hazard Identification: Identify a pathogen and the disease it causes, including symptoms, severity, and death rates. Identify sensitive populations that are particularly prone to infection. In New Zealand, rotavirus has been used because good clinical trial data and associated dose-response relationships are available. Rotavirus is also one of the most UV-resistant viruses implicated in water-borne disease outbreaks, it is a hazard for humans, and is a good representative of other pathogens (McBride 2008a). Infection can arise from shellfish ingestion, as well as accidental water ingestion. However, there is some uncertainty whether it adequately represents norovirus, which has a very low infectious dose (Palliser 2009b). Dose-Response: Data sets from human studies allow the relationship between the dose (number of microbes) received and the resulting health effects to be quantified, and allows the construction of mathematical models to predict dose-response. In the application of QMRA in New Zealand, the more conservative risk of infection is characterised rather than the risk of illness. Exposure Assessment: Describes the pathways that allow a microbe to reach people and cause infection (e.g., by ingestion). The size and duration of exposure by each pathway needs to be determined. In the application of QMRA in NZ, model variables and inputs include: 1) the virus concentration in the sewage plant influent; 2) efficacy of the treatment plant; 3) mixing factors; 4) duration of swim event; 5) ingestion rate of water during swimming; 6) shellfish consumed; 7) bioaccumulation factor for the microbe in shellfish. Predicting transport of microbes has been carried out using particulate transport/hydrodynamic models, which also allow for die-off. Exposure is usually characterised at accessible areas used for recreation (e.g., at beaches, shellfish gathering sites). In addition, the risks associated with the infrequent occurrence of extreme microbial concentrations have been calculated, i.e., when a community-wide viral illness has occurred (Palliser 2009b). Risk Characterization: The information from the steps above is integrated into a mathematical model to calculate risk - the probability of an outcome of infection. Monte Carlo Analysis is used to generate a risk profile including average and worstcase scenarios. QMRA could be specified when estimates of the health risks associated with wastewater discharges are required. 6 Centre for Advancing Microbial Risk Assessment Technical aspects of integrating water quality science in freshwater and coastal environments 75

86 6.3.4 Direct measure of pathogens Rather than measure indicators of human pathogens, another approach involves direct measurement of specific pathogens. Currently this approach is used mainly in research studies, and the prognosis for application to routine monitoring is summarised below. A three-year study was initiated in 1997 to investigate microbial contamination in New Zealand water bodies (McBride et al. 2002). Although this study focussed on surface fresh water sites throughout New Zealand, they are still relevant because freshwater inflows are the main source of contamination of marine water. Four microbial indicators and six highly relevant pathogens (enteroviruses, adenoviruses, Cryptosporidium oocysts, Giardia cysts, Salmonellae and Campylobacter) were monitored. The Campylobacter detection rate was 60%, virus pathogens were detected in about one-third of all samples, the Salmonellae detection rate was low (10% of samples), while Giardia and Cryptosporidium cysts were detected infrequently (8% and 5% respectively). The main outcomes of this risk assessment study were that, of the pathogens assessed in this study, Campylobacter and adenoviruses are the most likely to cause human waterborne illness to recreational freshwater users. An estimated 5% of total notified campylobacteriosis in New Zealand could be attributed to water contact recreation. Land use within the study catchments showed that bird catchments were the most contaminated across nearly all micro-organisms. Dairying catchments were often the second most contaminated with pathogens, but not for Campylobacter or adenoviruses. The municipal and forestry/undeveloped catchments were generally the least contaminated. Campylobacter Campylobacter is a human-specific zoonotic pathogen, largely derived from dairy cows. It is therefore an indicator of human health risk and contamination of waterways by dairy cows. It is, however, difficult to measure. It could be developed as an indicator once when stable, routine analytical methodology becomes available. Viruses Direct measures of human adenoviruses and retroviruses are indicators for human viral pollution, discharges from septic tanks and poor wastewater treatment plant (WWTP) treatment efficacy. However, they are very difficult and costly to monitor. Major issues at present are with analytical methodology, which keeps changing (and improving), therefore the results from different methods or over time are not directly Technical aspects of integrating water quality science in freshwater and coastal environments 76

87 comparable. It is probable that this indicator (including norovirus in QMRA) will become more widely applied in the future Drinking water Explicit water-quality standards for drinking-water sources do not exist, it being assumed that water treatment systems can provide adequate treatment to ensure that reticulated water complies with the New Zealand Drinking Water Standards. The degree of treatment required does therefore require knowledge of the degree of microbial contamination of the source waters Shellfish tissue: FSANZ (Food Standards Australia and New Zealand 2005) Standard 1.6.1: uncooked bivalve molluscs No more than 1 of 5 replicates >100 E. coli per 100 g. No replicates >1000 E. coli per 100 g. Standard 1.6.1: cooked bivalve molluscs No more than 1 of 5 replicates >10 E. coli per 100 g. No replicates >100 E. coli per 100 g. [The previous standard was no more than 2 of 5 replicates >230 FC per 100 g, none >330 per 100 g (MOH 1995)] Overview and new related developments This review/critique summarises the rationale for the E. coli criteria, the robustness of the MfE and NOF guidelines and points to other indicators and assessment techniques (such as Quantitative Microbial Risk Assessment, QMRA) when monitoring gives ambiguous results or where discharge of treated wastewater is involved. Other useful methods commonly used in research (e.g., Microbial Source Tracking), offer possibilities for future monitoring and risk assessment. Another recent development with potential is prediction of indicator loads using catchment runoff models that account for sources (number and types of animals) and attenuation of microbes (e.g., from best management practices). Although in its infancy, this approach could be developed to provide a basis for a limits-type approach (e.g., limiting the total load of indicator bacteria in different reaches of rivers). These are described as follows. Technical aspects of integrating water quality science in freshwater and coastal environments 77

88 Catchment sources and modelling loads Indicator organism loads and concentrations can be calculated by using the CLUES package (Catchment Land Use for Environmental Sustainability, (Semadeni-Davies et al. 2009)). At present CLUES predicts average annual E. coli loads and is being developed to estimate the effect that implementation of management practices may have on indicator organism loads and concentrations. Recently, median concentrations of E. coli in parts of New Zealand were calculated for the period (Unwin et al. 2010). Faecal Source tracking Faecal Source Tracking is commonly practiced overseas to investigate indicator exceedances and has been applied in New Zealand (Devane et al. 2010). Overseas faecal contamination issues are related to management of sources, the difficulty of managing diffuse sources - especially in undeveloped lands, multiplication of indicators organisms within the aquatic environment (and expectation that most of these non-human sources do not constitute a health risk). However, in New Zealand, there is strong evidence that animal sources (birds and ruminants) constitute health risks. Therefore, it is unlikely that Faecal Source Tracking will become part of human health risk guidelines, but it will continue to be used as an investigative tool to greater understanding of sources and their management, and refining human health risk assessments. 6.4 Relevance/suitability for Auckland Faecal indicator bacteria (E. coli) monitoring is currently undertaken monthly at 34 river and stream sites for SoE monitoring, but this parameter is not one of the seven parameters included in the Auckland WQI calculation (Lockie et al. 2013). In 2012 there were 27% of the sites which exceeded the annual median value of 1000 cfu/100 ml which is the NOF standard for secondary contact recreation (MfE 2014a). Specific microbial monitoring studies have been undertaken in coastal freshwater lagoons which are considered regionally important because of their high recreational use. The West Coast lagoons at Karekare, Piha, North Piha and Te Henga have formed where their freshwater and marine environments interact. These lagoons have been monitored under the council bathing beach Safeswim programme in accordance with the Ministry for the Environment (MfE) and Ministry of Health (MoH) national guidelines (MfE/MoH 2003) since summer , with data indicating that they would be graded very poor because of their history of poor water quality. A pilot study was undertaken in to identify the biological sources of the faecal pollution of the West Coast lagoons (Noble 2014). The results of that study showed that a range of animal faecal sources were polluting the Technical aspects of integrating water quality science in freshwater and coastal environments 78

89 lagoons which were originating from human (septic systems), dogs, wildfowl, livestock and unidentified sources. The findings of the study indicated that a range of site-specific measures will be required to provide suitable water quality for primary contact recreation. Microbiological pollution from wastewater outfalls and diffuse source pollution is a key issue in Auckland. For urban areas, combined sewer overflows, designed overflows (from reticulation overloads especially) and contamination of waterways as a consequence of cross connections between stormwater and sewage systems cause significant microbiological pollution. In pastoral areas, dairy farming and dry stock farming represent the greatest threat to the microbiological quality of rural streams. Management will need to continue addressing these issues and conduct microbiological monitoring, especially in situations where faecal contamination is likely catchments receiving treated sewage, urban streams and stormwater runoff, and catchments with pastoral areas. 6.5 Recommendations The NOF bands for secondary contact are mandatory, while the bands for primary contact are optional. The council and community will need to decide the importance of assessing primary recreation in Auckland s freshwaters. The current MfE criteria (see Section 6.2) are appropriate for Auckland bathing beaches. While widely used in Auckland for marine bathing beaches, the grading approach is not used at fresh water sites. In most cases, monitoring results for E. coli are assessed by comparing the magnitude of E. coli concentrations against MfE (2003) surveillance/alert/action levels, but the management actions associated with these levels are not activated. This monitoring and assessment approach will be well suited to the NOF Attribute bands. Catchment modelling, which is in its infancy for this application, should be continued to be developed, to see if this will yield a robust catchment-specific limit-based approach to managing microbiological pollution. The MfE (2003) criteria also include a catchment sanitary assessment, which although not a true limits-based approach, is probably useful for assessing catchment sources, and when dealing with a number of very complex sources and processes. As described previously, problems generally occur downstream of significant wastewater overflow problems, or in catchments subject to these discharges. Monitoring should be carried out near wastewater outfalls, to ensure treatment is adequate to reduce risk associated with contact recreation to acceptable levels. Technical aspects of integrating water quality science in freshwater and coastal environments 79

90 QMRA should continue to be used to assess health risks associated with sewage discharges. Genotyping approaches appear very promising and Auckland Council should keep a watching brief on overseas developments of these methods. Technical aspects of integrating water quality science in freshwater and coastal environments 80

91 7 Stream Ecological Valuation (SEV) 7.1 Overview and importance A critical part of improving the ecological integrity 7 of rivers is accurate assessment of current ecological state so that causes of degradation, or the success of rehabilitation efforts, can be measured. River monitoring has traditionally concentrated on the measurement of structural indicators (such as water quality and the number and type of aquatic organisms). Structural indicators focus on patterns of abiotic characteristics or biological community composition, whereas functional indicators are measures or estimates of the rate of processes occurring in an ecosystem. In other words, structural indicators assess the physical, chemical and biological state of an ecosystem, while functional indicators assess the ability of an ecosystem to provide certain services or functions. Since ecological integrity includes both the components and the processes of an ecosystem, river monitoring should include both structural and functional indicators in order to adequately assess ecological integrity (Young et al. 2008). An advantage of the functional approach is that a common set of functions can be identified that applies to a wide variety of stream and river types across a range of geographic locations. This set of stream functions can provide a common currency with which to compare streams that may differ in their biological composition or physical characteristics. In addition, by assessing ecosystem services, the functional approach implicitly estimates the ecological value of a stream reach to the wider stream network, rather than simply assessing its ecological condition. The Stream Ecological Valuation (SEV; (Storey et al. 2011)) uses an ecological function perspective to assess the integrity and value of Auckland region s streams. Although it assesses structural components of a stream reach rather than directly measuring ecological processes, it interprets these components in terms of their ability to perform ecological processes. SEV was developed in order to understand the ecological consequences of piping an estimated 9 km of headwater streams per year across the Auckland region, and to 7 Here we use the same definition of ecological integrity as Schallenberg et al. (2011): The degree to which the physical, chemical and biological components (including composition, structure and process) of an ecosystem and their relationships are present, functioning and maintained close to a reference condition reflecting negligible or minimal anthropogenic impacts. This means full integrity is attained when human actions have little or no influence on sites. This definition distinguishes ecological integrity from ecosystem health, which assesses the state of an ecosystem in terms of the stresses put on it, and its ability to keep providing products and processes for both economic and ecological means. In this context, ecosystem health indicates the preferred state of sites that have been modified by human activity, ensuring that their ongoing use does not degrade them for future use (Karr 1999). Technical aspects of integrating water quality science in freshwater and coastal environments 81

92 determine appropriate environmental compensation in cases where piping or other activities likely to compromise a stream reach were unavoidable. Adopting the same approach that underpins the no net loss of wetlands policy in the United States, a set of ecological functions relevant to Auckland streams was identified by a panel of expert scientists. Two reports (Rowe et al. 2008; Rowe et al. 2006) document the original 16 ecological functions and a robust method of quantifying them developed by the expert panel. A third report (Storey et al. 2011) updates the method with a slightly reduced number of functions and some slightly simpler formulae. The methodology was originally developed for streams in Albany (Rowe et al. 2006), but is now routinely applied across the Auckland region for State of the Environment monitoring (see Auckland Council freshwater report cards in reference list), across Greater Wellington region for resource consent applications, and in Hawke s Bay for prioritising streams for rehabilitation. SEV identifies ecological functions in the following categories: hydraulic functions (i.e., processes associated with water storage, movement and transport) biogeochemical functions (i.e., those related to the processing of minerals, particulates, and water chemistry) habitat provision functions (i.e., the types, amount, and quality of habitats that the stream reach provides for flora and fauna) native biodiversity functions (i.e., the occurrence of diverse populations of indigenous native plants and animals that would normally be associated with the stream reach). The specific ecological functions considered important for Auckland stream reaches within these broad categories are listed in Table 7-1. To assess the performance of each ecological function listed in Table 7-1, a number of relevant variables are scored between 0 and 1, according to their condition. These variables are not direct measures of ecological processes (unlike the variables described by Young et al. (2008)). Rather they are observable features of a stream reach that indicate how well ecological functions are being performed within the reach. The variables are chosen to be easily measurable so that the methodology can be widely utilised and completed rapidly with minimal equipment. They do not include any actual measurements of water quality. The final step in the SEV process is to average the various functions, producing a single score, which allows comparison of performance of the ecological functions in one stream reach to that in other reaches. The methodology and algorithms are provided in the Stream Ecological Valuation (SEV) technical reports and user guide (Neale et al. 2011; Rowe et al. 2008; Rowe et al. 2006; Storey et al. 2011). Results for each reach are Technical aspects of integrating water quality science in freshwater and coastal environments 82

93 compared against reference values for natural or undisturbed streams, making SEV a measure of ecological integrity rather than ecosystem health (see footnote on previous page). Table 7-1 The 14 functions in Stream Ecological Valuation, grouped according to type. Function type Function Hydraulic Natural flow regime Flood plain effectiveness Connectivity for species migrations Connectivity to groundwater Biogeochemical Water temperature control Dissolved oxygen maintenance Organic matter input In-stream particle retention Decontamination of pollutants Habitat provision Fish spawning habitat Habitat for aquatic fauna Biodiversity Fish fauna intact Invertebrate fauna intact Riparian vegetation intact 7.2 Use/applicability SEV was originally designed for use in resource consent applications for assessing the loss of ecological function in a stream network when particular stream reaches were piped or otherwise degraded by urban developments. As part of this process, SEV scores are used to determine Environmental Compensation (EC), which is more commonly referred to as offset mitigation in the international literature. EC is used to offset the unavoidable residual impacts of an activity once all practical steps have been taken to minimise adverse effects. The compensation is typically applied to a different stream than the stream being developed. The advantage of the function-based approach of EC is that the functions provide a common currency for calculating an appropriate compensation when the biological, physical or chemical characteristics of the impact reach differ from those in the compensation reach. The Technical aspects of integrating water quality science in freshwater and coastal environments 83

94 SEV Guidelines provide an equation for calculating the length of stream reach that must be rehabilitated given the expected improvement in SEV score resulting from the proposed rehabilitation strategy at the compensation reach and an expected decline in SEV score at the impact reach. Impact site Compensation site Before After Before After ECR = (0.38 / 0.22 ) x 1.5 ECR = 1.73 x 1.5 ECR = 2.6 Figure 7-1 A schematic diagram illustrating the process for calculating an Environmental Compensation Ratio (ECR) from the expected loss of ecological function at an impact site and the expected gain through rehabilitation works at a compensation site. The final ECR refers to the ratio of stream length that must be rehabilitated relative to the length impacted. The SEV is now used for a variety of other purposes as well. For example, for the past several years Auckland Council has used SEV to assess the ecological integrity of 82 stream sites in its region-wide State of the Environment monitoring programme. Another application of SEV is to prioritise stream reaches for rehabilitation and determine the most strategic forms of rehabilitation. SEV allows managers to quantify an expected improvement in individual ecological functions or overall ecological integrity resulting from proposed rehabilitation works. By comparing the rise in SEV score among different sites arising from different rehabilitation strategies, and relating these to the cost of each, candidate sites and rehabilitation works can be ranked according to cost-benefit (e.g., Storey and Croker (2010)). Technical aspects of integrating water quality science in freshwater and coastal environments 84

95 Table 7-2 Guidelines for the suitability of SEV in different stream types that occur in Auckland (from Storey et al. 2011). Stream type Saltwater influenced Tidally influenced Wetlands (stream channel not well-defined) High gradient streams Lake-fed streams Spring-fed streams Intermittent streams Fourth-order and larger rivers Applicability of SEV Do not use Can be used where stream water is backed-up by high tides but above saltwater influence. Data should be collected around low tide Do not use OK to use OK to use OK to use Intermittent streams - use with caution (see Storey (2010) for potential issues SEV performance not tested, but could be used if suitable reference data were collected 7.3 Critique/review of SEV approach for stream water management At present there are no published guidelines for categorising SEV scores as poor, fair, good or excellent. However, in their State of the Environment report cards, Auckland Council report SEV results in terms of letter grades from A to F, based on a large database of sites with SEV scores to provide reference sites and assessments of levels of impact (Auckland Council 2014b). The freshwater SoE reporting provides an overall grade made up of five indicators: a water quality index (WQI; based on temperature, oxygen concentration, turbidity, ph, ammonia and nutrients (nitrogen and phosphorus)) (Lockie et al. 2013); and four SEV indicators (flow patterns, nutrient cycling, habitat quality, biodiversity) (Auckland Council 2014b) Strengths 1. SEV combines a range of physical and biological attributes (and, by inference, chemical processes) into a single score. It is thus a composite index, providing a holistic assessment of stream ecological condition. 2. The individual function scores underlying the single SEV score can be extracted and used as guidelines for invertebrate community integrity, fish community integrity/fish migration, etc. Some functions may provide information relevant to values such as aesthetics, cultural health and natural character. 3. SEV is already being used for SoE monitoring across Auckland region. Technical aspects of integrating water quality science in freshwater and coastal environments 85

96 4. SEV scores are easily communicated in report card fashion using the four broad categories of ecological function. Examples are available on the Auckland Council website (see reference list for web links). 5. SEV discriminates well between levels of human impact. Among the 82 sites in Auckland Council s State of the Environment monitoring network to date, reference sites (relatively natural or unmodified) have had SEV scores between 0.76 and Sites in exotic forest have scored between 0.59 and 0.82, those in rural catchments have scored between 0.42 and 0.79, and urban streams have scored between 0.36 and 0.70 (Fig. 7-2). 6. In addition to discriminating levels of impact, SEV functions indicate the local drivers of degraded ecological integrity. This information is crucial for developing rehabilitation strategies SEV score Reference Forestry Rural Urban Figure 7-2 Scores for sites in Auckland s State of the Environment monitoring network grouped according to the main land use in the catchment. Box plots show median (central line), 75 th percentile (top and bottom of boxes) and 95 th percentile scores ( whiskers ). Technical aspects of integrating water quality science in freshwater and coastal environments 86

97 7.3.2 Limitations 1. SEV does not include any direct measures of water quality, therefore it cannot be related to human/animal health guidelines or the impact of other abstractive uses. Also, SEV cannot be used to directly assess the impact of loads of contaminants such as silt, nutrients or toxicants to receiving waters (though it will indicate the capacity of individual stream reaches to reduce the passage of such contaminants from upstream sources). Auckland Council Freshwater Report Cards therefore add water quality measurements to SEV assessments in order to provide a complete picture of stream ecological integrity. 2. It is not as widely used as other biological indices across New Zealand. However, it does contain Macroinvertebrate Community Index (MCI), EPT richness and Fish Index of Biological Integrity (IBI) which are widely used biological indices (see later sections for definitions of these). 3. Most SEV functions assess the drivers of ecological functions rather than measuring the functions or processes directly. Thus it assumes there are fixed relationships between the drivers (human modifications of streams and their surroundings) and ecological responses (lowered performance of ecological functions). This is a reasonable assumption, but there may be cases where mitigation measures may alter the relationship. 4. SEV focuses on individual stream reaches and their immediate riparian zones. Thus, while it can assess local-scale drivers of degradation, it does not attempt to assess drivers at larger scales such as the catchment scale. Many drivers of degradation, particularly in urban streams but also in rural streams, occur at the catchment scale, and only limited improvements in ecological integrity may be achieved by reach-scale restoration. 5. Because SEV focuses more on the drivers of ecological functions than on response variables, it may overestimate the changes in ecological integrity resulting from reach-scale modifications (restoration or urban development), and underestimate changes resulting from catchment-scale modifications. 7.4 Relevance/suitability for Auckland The SEV is currently used in 34 Auckland rivers and streams as part of the monthly SoE monitoring (Auckland Council 2014b). As the name suggests, the Stream Ecological Valuation is designed for streams only, and is not suitable for assessing lakes, wetlands, groundwaters or estuaries. SEV was developed specifically for Auckland streams and is acknowledged to be suitable for most stream types that occur across the Auckland region, including hardand soft-bottomed streams. The table in Storey et al. 2011, summarises the guidelines for using SEV in different stream types. In all cases where SEV is used for Technical aspects of integrating water quality science in freshwater and coastal environments 87

98 different stream types or geographic area, reference data must be collected for the same stream type as the test sites in order to correctly calculate certain variables (e.g., invertebrate variables) and interpret the final SEV scores. The River Environment Classification (REC; and Freshwater Environments of New Zealand (FENZ) can be used to identify stream types and locate suitable reference sites. The like-with-like principle should also be followed when comparing SEV scores among test sites. SEV scores should be broadly comparable across the different stream types for which it has been tested, however, great care must be exercised when comparing individual functions among very different stream types. 7.5 Recommendations SEV is highly relevant as an integrated measure of stream ecological integrity, incorporating biological and physical attributes and (inferred) chemical processes. Appropriate bands would need to be developed for specific land use classes before it could be used as a management measure for ecological health or natural state. Technical aspects of integrating water quality science in freshwater and coastal environments 88

99 8 Macro-invertebrate Community Index (MCI) 8.1 Overview and importance Preamble: biological indices using macroinvertebrates The Macroinvertebrate Community Index (MCI) is one of a number of indices used for summarising and condensing the large amount of information contained in data sets derived from stream macroinvertebrate monitoring. Other indices describe different aspects of the macroinvertebrate community, for example its species diversity, the abundance of the whole community or particular species groups, or the percentage of groups with different ecological roles (see section 15, Other indices; Table 15.1). Each index may respond differently to different types of human-induced impact, and some are designed to reflect very specific types of impact (for example, the percentage of leaf-shredding insects responds strongly to the loss of forest cover). Because each index contains slightly different information about the community and the stresses it experiences, NEMaR recommends using several indices to report macroinvertebrate data. In this section, after discussing in general the use of macroinvertebrates for biological monitoring, we focus specifically on the MCI and its variants, as they are the indices most widely used for summarising macroinvertebrate data The use of macroinvertebrates as indicators of stream condition Macro-invertebrates are the group of organisms most commonly used for assessing river ecological condition (Rosenberg et al. 1993). This is because: Macro-invertebrates are sensitive to many forms of habitat and water quality degradation (e.g., temperature, fine silt deposition, macrophyte growth, organic pollution, dissolved oxygen, toxic contaminants, and extremes of ph). The different sensitivities of different taxa are reasonably well known so that robust indices of stream health 8 can be calculated from the presence and/or abundance of different taxa. Macro-invertebrates have limited mobility so they tend to reflect environmental conditions within a specific area, usually metres to tens of metres, which makes them suitable for assessing site-specific impacts. They integrate the effects of short-term environmental variations over longer periods. Because each animal lives in water for weeks or months, its presence indicates that environmental conditions must have been suitable during that entire period. In contrast, water quality monitoring typically 8 Stream health assesses the state of a stream in terms of the stresses put on it, and its ability to keep providing products and processes for both economic and ecological means. In this context, stream health indicates the preferred state of sites that have been modified by human activity, ensuring that their ongoing use does not degrade them for future use (Karr 1999) Technical aspects of integrating water quality science in freshwater and coastal environments 89

100 involves spot measurements that are likely to miss critical extremes, for example daily peaks in temperature, daily minima in dissolved oxygen, shortterm discharges of pollutants or stresses associated with storm flows. They are relatively easy to collect and identify without expensive equipment, and protocols for sample collection and processing are well established (Stark et al. 2001). Macroinvertebrates provide a direct measure of life-supporting capacity, which is a key attribute of fresh waters identified in the NPS-FM. For these reasons, benthic macro-invertebrates continue to be recommended for providing the core of river bio-monitoring programmes, both in New Zealand (e.g., (Collier et al. 2010; Davies-Colley et al. 2012b; Moore et al. 2008; Schallenberg et al. 2011)) and internationally (e.g., (Barbour et al. 1999; Hering et al. 2004)). In New Zealand, all regional and unitary councils except one conduct biomonitoring using macroinvertebrates (Davies-Colley et al. 2012b). Despite the advantages listed above, biomonitoring with macro-invertebrates does have some limitations. For example: Macroinvertebrate biomonitoring is used much less for lakes or wetlands than for streams, because the fundamental ecological relationships are less wellknown, and because it can be harder to define a homogeneous habitat for lake littoral areas than for streams (White et al. 2003). In New Zealand, no sampling protocols or indices exist for biomonitoring of lakes using macroinvertebrates. Because macroinvertebrates respond to a range of environmental conditions, it may not be clear from the macroinvertebrate composition what the main limiting stressor(s) in the system are. Some indices have been developed (mainly overseas) that use the macroinvertebrate data in particular ways to detect specific stressors (e.g., Hering et al. (2004)). For example, macroinvertebrate data can be viewed as the presence or abundance of traits, such as mode of respiration, locomotion or reproduction, rather than the presence or abundance of taxa (Phillips et al. 2012). Viewing the data in this way can give an indication of the specific stressors on the macroinvertebrate community, but it does not provide unequivocal evidence of the impact or absence of specific stressors. For this reason, macroinvertebrate data are most useful when used in combination with direct measures of water and habitat quality. Macroinvertebrates do not respond to all stressors that may affect aquatic life. In particular, because most do not require long-distance migrations, they are unlikely to respond to migration barriers that affect fish. Technical aspects of integrating water quality science in freshwater and coastal environments 90

101 Because macroinvertebrate monitoring is time-consuming and expensive, it is typically conducted only once per year. Therefore macroinvertebrates are not ideal for providing early warnings of short term impacts The Macro-invertebrate Community Index (MCI): Overview and importance The Macro-invertebrate Community Index (MCI) is a form of biotic index. Biotic indices are based on the concept that some macro-invertebrates are very sensitive to degraded habitat and water quality, whereas others have different levels of tolerance. Therefore, the extent to which a freshwater ecosystem is degraded may be estimated by examining the relative proportions of sensitive and tolerant macroinvertebrates. Biotic indices derive a single score by assigning a numerical value to each taxon that reflects their degree of tolerance to a stressor of interest, then averaging the tolerance values of all taxa present at a site. Biotic indices are used routinely in many parts of the world for summarising biological monitoring data and reporting it as a simple score. For example, in the UK, the standard biotic index for stream health is known as ASPT-BMWP (average score per taxon of the British Macroinvertebrate Working Party), and in Australia it is known as SIGNAL (Stream Invertebrate Grade Number Average Level). The MCI is the New Zealand equivalent of these indices, adapted for the New Zealand stream fauna. MCI is one index in a family of variants that use different forms of macroinvertebrate data and are relevant to different stream types. Whereas MCI is based on presence-absence data, its quantitative and semi-quantitative versions (QMCI and SQMCI, respectively) are calculated from the abundances of taxa QMCI from actual numbers and SQMCI from abundance categories (Stark et al. 2007a). MCI, QMCI and SQMCI are designed for use in hard-bottomed streams (those with beds composed mainly of hard substrates such as gravels, pebbles and cobbles), but a parallel system (referred to as sb-mci, sb-qmci and sb-sqmci) is available for scoring soft-bottomed streams (Stark et al. 2007b). The two systems differ only in the tolerance scores assigned to the macro-invertebrate taxa; the formulae used for calculating the overall indices are the same. The data underpinning the soft-bottomed scores were obtained from stream sites across Auckland region (Stark et al. 2007b). In the following discussion, MCI refers to the MCI family of indices, rather than MCI sensu stricto, unless otherwise stated. Technical aspects of integrating water quality science in freshwater and coastal environments 91

102 8.2 Use/applicability MCI was originally developed to assess organic pollution of hard-bottomed streams in the Taranaki region (Stark 1985). However, since then MCI has been shown to work well in other parts of New Zealand, and to reliably discriminate sites along gradients of human impact that include both pastoral development and urbanisation (Collier 2008; Stark et al. 2007b). This is despite the fact that pastoral development may be associated with a variety of different stressors (e.g., silt deposition, excessive periphyton growth, increased temperature), and urban stressors differ markedly from pastoral stressors. For this reason, MCI and its variants are the main indices used by New Zealand s regional councils for State of the Environment reporting (at least 13 of 15 councils that collect macro-invertebrate data use the MCI and/or its variants (Davies-Colley et al. 2012b). MCI can be used only for wadeable streams, not for lakes, estuaries, groundwaters or large (non-wadeable) rivers. A wetland MCI is under development, but is not likely to be available soon. 8.3 Critique/review of the MCI approach for assessing ecological health MCI is an integrative measure of macroinvertebrate response to both habitat and water quality conditions in the stream. As such, it does not identify the stressor that is causing the adverse effect and MCI scores should be determined for reference sites with suitable macroinvertebrate habitats. Auckland Council have proposed the MCI score for rivers and streams in four land use classes (native forest, exotic forest, rural areas and urban areas) 9 as part of its Proposed Auckland Unitary Plan (Auckland Council 2016). MCI is not suitable for assessing impacts of toxic chemicals such as metals (Hickey et al. 2002) and probably not suitable for assessing the impacts of specific pollutants arising from urban catchments. It is also not suitable for assessing hydrological changes due to water abstraction/diversion or following change to the extent of impervious surface in a catchment (Stark et al. 2007a). Condition bands for MCI score denoting excellent, good, fair and poor stream condition are established and generally agreed for stony (hard-bottom) streams (Stark 1985; Stark et al. 2007a). A MCI has also been developed for soft-bottom streams (Stark et al. 2007b). A system of condition bands for MCI appears compatible with the NOF framework, and has been proposed for consideration 9 The proposed MCI guidelines for Auckland rivers and streams are: native forest, 123; exotic forest, 111; rural areas, 94; and urban areas, 68 (section , Table 1; Auckland Council 2014a). Technical aspects of integrating water quality science in freshwater and coastal environments 92

103 (Collier 2014) 10. Collier et al. (2014) noted that: (i) while the MCI (including its hardand soft-bottom derivatives) is not considered conceptually to be the most up-to-date science for a macroinvertebrate measure, the measures that might be more appropriate were not considered to be ready for inclusion in the NOF, mainly because of limitations in reliably estimating reference condition; (ii) it should be noted that presence-absence indices like the MCI are potentially more effective at detecting improvements in quality rather than deterioration because it only takes one individual of a new taxon to potentially raise the score, whereas a whole population of a taxon would need to be lost to see a decline; and (iii) that the advantage of MCI as an overall indicator of Ecosystem Health that it integrates a wide range of stressors in turn presents challenges for identifying appropriate limits and management responses. MCI is therefore considered more suitable as a performance measure and to trigger investigation of which stressors are causing the responses measured. The MCI was not incorporated in the 2014 NOF standards (MfE 2014), but will be considered for future legislative updates Strengths MCI has been shown to discriminate reasonably well among sites that vary in their degree of rural and urban impact (land cover gradients). Condition bands are well established and generally accepted though there may be considerable overlap between land use classes. Taxa tolerance scores are generally established and accepted. MCI scores at reference sites are reasonably stable over time, i.e., MCI is not very sensitive to natural variation (e.g., (Collier 2008; Stark et al. 2007a)). QMCI is somewhat more variable in this respect. It is particularly sensitive to preceding flow conditions, as floods may markedly reduce numbers of invertebrates (Quinn et al. 1990b). Almost all regional councils in New Zealand use MCI for State of the Environment reporting, so results in Auckland can be evaluated in a national context Weaknesses Any single metric loses the large amount of information that is contained within the original multi-species data set. MCI suffers this problem no less than any other metric. 10 The proposed NOF bands are based on the thresholds already widely adopted in use of the MCI throughout New Zealand: >120 (for A band), (for B band) and (for C band) with a national bottom line of 80. Assessments of condition within the WMU would be made on the basis of a two year rolling mean using standard collection methods (Collier et al. 2014). Technical aspects of integrating water quality science in freshwater and coastal environments 93

104 While strong correlations have been found between MCI and certain impact gradients related to land cover (e.g., fine sediments (Niyogi et al. 2007)), MCI scores are not responsive to other types of impact, e.g., altered hydrology, toxic chemicals (especially from point source discharges). MCI performed less well than another macroinvertebrate metric (%EPT abundance) and a multimetric Average Score per Metric (ASPM) at detecting low levels of urban and rural impact among 511 Waikato stream samples (Collier 2008). MCI indicates only the condition of the stream reach sampled, and cannot indicate downstream effects as it does not reveal which stressors most affect the macroinvertebrate community. 8.4 Relevance/suitability for Auckland MCI and SQMCI can be calculated from the semi-quantitative macroinvertebrate data currently collected by Auckland Council as part of its SoE Monitoring programme. Auckland Council currently produces MCI scores for all monitored streams as a component of the SEV, which is its main SoE reporting tool. Auckland streams are predominantly soft-bottomed (sb), therefore most require the sb-mci scores to be applied. Sb-MCI tolerance values were derived from a data set of sites across the Auckland region, and sb-mci site scores have been shown to be significantly correlated with gradients in urban and rural land use, and with a variety of water and habitat quality variables (Stark et al. 2007b). Therefore, the sb-mci system should be highly suitable for assessing the degree of degradation in Auckland streams. 8.5 Recommendations MCI is recommended alongside measures of water quality and habitat quality for summarising the ecological health of macroinvertebrate communities in Auckland streams. The soft-bottomed version of MCI (sb-mci) should be used in place of the hb-mci for naturally soft-bottomed streams, which probably comprise the majority of Auckland streams. MCI is best used in combination with QMCI or SQMCI, as the latter are able to detect small and medium changes in stream health. In addition, other biotic indices such as Total taxa richness, EPT taxa richness and %EPT abundance should be used (Davies-Colley et al. 2012b), as these show different aspects of the macroinvertebrate community (i.e., structure and composition in addition to tolerance), and they may be sensitive to impacts to which the MCI is not (Collier 2008). Technical aspects of integrating water quality science in freshwater and coastal environments 94

105 A combined index such as Average Score Per Metric (Collier 2008) or the Invertebrate Fauna Intact function from SEV may perform better than MCI or any other single index in discriminating sites at all levels of human impact (Collier 2008). Technical aspects of integrating water quality science in freshwater and coastal environments 95

106 9 Bacterial Community Index (BCI) 9.1 Overview and importance Stable bacterial communities are found living within biofilms on all surfaces within streams. Biofilms consist of a microbial community composed of bacteria, fungi, algae, viruses, protozoans, nematodes and other picoinvertebrates, all living within a protective, adhesive matrix of polymeric substances (Lewis et al. 2010). Biofilms play very important roles in freshwater ecosystems. They are major sites for primary production, and nutrient and carbon cycling (Lear et al. 2012). In addition, they can accumulate toxic contaminants, such as metals in urban stormwater, then transform or transfer them to higher trophic levels. The microbiota, along with the non-living matrix, are high in lipids and proteins, thus are a nutrient-rich food for macroinvertebrates and fish. Human activities may alter the composition of biofilm community, which may in turn cause degradation of the whole stream ecosystem because of these important ecological roles that biofilms play. Biofilm bacteria are potentially good biological indicators of stream condition because their species composition responds to environmental conditions in a similar way to other biological indicators such as macro-invertebrates. Bacterial communities possess many of the same attributes as macro-invertebrates, e.g., they remain in the same location (so respond to local environmental conditions), can integrate water and habitat quality conditions over time, are very diverse in terms of species and functions, and include species groups that are variously tolerant and sensitive to pollution (Lewis et al. 2010). However, there are some important differences between bacterial biofilms and macroinvertebrates. Bacteria occupy a lower level of the food chain than macroinvertebrates, where they are very active in energy, carbon, nutrient and contaminant cycling. Also, unlike macroinvertebrates, the bacterial community is always very diverse, even in habitats with very poor water quality or habitat quality (e.g., concreted channels). For these reasons, a Bacterial Community Index (BCI) could provide a useful measure of stream health that supplements other measures (invertebrates, fish, water quality, physical habitat). A BCI for New Zealand was developed by Lewis et al. (2010). It was based on a molecular description (ARISA; Automated Ribosomal Intergenic Spacer Analysis) of the bacterial biofilm community collected from 254 stream sites in seven regions (Auckland, Waikato, Hawke s Bay, Manawatu, Greater Wellington, Tasman and Canterbury). Lewis et al. (2010) compared the bacterial community profile in each stream with the Macroinvertebrate Community Index (MCI) score of the same site to develop a model relating a subset of the bacterial community to stream ecosystem Technical aspects of integrating water quality science in freshwater and coastal environments 96

107 health. The model, called the BCI, organised the bacterial community to best predict the MCI score of each stream. The BCI is an indication of the dominant species within the community and the functions present. Streams with lower BCI are dominated by bacterial species and strains associated with (i.e., more tolerant of) higher levels of contaminants or other impacts, whereas those with higher BCI are dominated by bacteria associated with lower-impact (more natural) conditions. 9.2 Use/applicability The field sampling method is relatively easy, involving a standard protocol. At each site, five rocks are each rubbed with a Specie-Sponge, which are then placed in a plastic bag and frozen. Samples are stable at this stage. A microbiology lab then performs the ARISA analysis on each sample according to standard protocols. The BCI developed by Lewis et al. (2010) performed reasonably well in predicting MCI score, an independent measure of stream condition. It was also able to differentiate streams in four different land use types: urban, rural, exotic forest and native forest. Ancion et al. (2014) also conclude that bacterial community composition is a sensitive indicator of environmental changes in freshwater systems, and an efficient indicator to monitor water quality in networks of enclosed stormwater pipes. The BCI can be used in any type of stream environment where hard surfaces are present. The range of environments therefore includes concrete channels, stormwater pipes or other stormwater structures where macroinvertebrates and fish bio-indicators are unlikely to be present (Ancion et al 2014). The BCI has been developed only for streams, and an equivalent is not yet available for lakes or other freshwater bodies. 9.3 Critique/review of BCI Within the range of possible BCI values (between 0 and 20), Lewis et al. (2010) defined four condition bands: poor (<7.9), medium ( ), good ( ) and high (>12). However, they also comment that interpretation of BCI data (as well as the BCI itself) requires further discussion. Therefore it appears likely that these condition bands may change over time. The BCI is designed to be applicable across New Zealand. However, Lewis et al. (2010) did find significant differences in bacterial community profile among the seven regions they sampled, i.e., a component of the bacterial community is regionspecific. In fact, regional differences were stronger than differences among land uses. Technical aspects of integrating water quality science in freshwater and coastal environments 97

108 9.3.1 Strengths The BCI has the following advantages over other biological indicators: Potentially more rapid response to changing environmental stressors (e.g., Ancion et al. (2014) found significant changes in bacterial community only three days after exposure to common heavy metal contaminants in stormwater). The bacterial community may contain up to 350 different genetic components (average 166), which is considerably higher than the likely number of macroinvertebrate taxa in a sample. This means that, particularly among sites of very low environmental quality, the BCI may discriminate sites better than MCI or fish. Samples may be collected from sites where other biological indicators (macroinvertebrates and fish) are not present (e.g., concreted channels). Sample collection and processing are economical. Sample analysis is rapid. Sample collection results in minimal site disturbance, therefore the same site may be sampled repeatedly without requirement for recovery. BCI responds to both organic and inorganic pollution (compared with macroinvertebrates, which respond strongly to both water quality and habitat variables) Limitations The main limitations of the BCI relate to its novelty, limited application to date, and requirements for further investigation. For example: In addition to species that may be associated with natural or with impacted or contaminated conditions, there are also cosmopolitan species and regionspecific species. Species belonging to each of these groups need to be better identified. The BCI may perform better once cosmopolitan and region-specific species are eliminated from analyses, because these add noise. Protocols for interpreting BCI values in terms of ecosystem quality still need to be developed. While very low and very high BCI values are easy to interpret, interpretation of mid-range values are not as clear. Urban and poor quality sites were under-represented in the 2010 survey, so more work is needed to evaluate and improve performance of BCI in these types of site. The sensitivity of the BCI at high quality sites could also be improved. Seasonal changes in the bacterial community profile need to be investigated (data in the 2010 survey are based only on mid- to late-summer samples). Technical aspects of integrating water quality science in freshwater and coastal environments 98

109 Stability of BCI values over longer time-scales (between years) must be tested. Initial results from Lewis et al. (2010) suggest some components of the bacterial community respond differently than macroinvertebrates to environmental stressors. The reasons for these differences need to be explored. Note that some of these investigations may have been done already. The most recent report on the BCI is Lewis et al. (2010), and more recent work is yet to be published. 9.4 Relevance/suitability for Auckland Auckland was one of the seven regions included in the survey by Lewis et al. (2010). Therefore, the BCI should be applicable to Auckland, noting that in the BCI model developed by Lewis et al. (2010), intra-regional differences in the bacterial community were significant. In other words, the BCI may still need some refinement for it to perform at its best in a given region. Also, this BCI model was based on relatively few samples collected from urban sites, so may not be optimised for urban stream applications. 9.5 Recommendations The BCI has shown promise, but we do not recommend that the BCI is used at this time. Further research is needed to clarify the following: 1. Is it useful at highly degraded or modified sites (including stormwater pipes and treatment structures) where few or no macroinvertebrates or fish are present? 2. Does it respond sensitively over a wide variety of sites to detect responses to improving or declining water quality in response to urban developments or restoration works? The BCI is still in development it will be wise to wait until further studies are completed before adopting it for monitoring purposes. Technical aspects of integrating water quality science in freshwater and coastal environments 99

110 10 Stream Macrophytes 10.1 Overview and importance In streams, growth of submerged, emergent and floating plants (together known as macrophytes) is very limited beneath intact native bush cover, which represents the natural condition of most Auckland streams. At low or moderate levels, macrophytes may be regarded as benefitting streams by increasing water retention during the dry season (Champion et al. 2000), providing habitat for periphyton, invertebrates and fish, and reducing the downstream transport of fine sediment and nutrients. However, proliferation of macrophytes is considered a form of ecological degradation, because the plants increase flooding risk, may produce extreme fluctuations in dissolved oxygen and ph, and reduce the aesthetic and recreational appeal of waters. Macrophytes are useful to monitor in streams because they both indicate modified conditions and themselves influence stream hydrology, water quality and physical habitat. Macrophytes proliferate under (hence indicate) conditions of low shading, slow current velocity (less than about 0.5 m/s) and low frequency of scouring floods (Matheson et al. 2012). These conditions typify low-gradient or spring-fed streams where agricultural or urban development has removed riparian forest. Macrophytes influence stream conditions as described above. Macrophytes are highly visible, and dense or widespread growths in stream channels are generally considered undesirable by ecologists and the public. In addition, a number of macrophytes (e.g., Egeria densa, hornwort Ceratophyllum demersum, alligator weed Alternanthera philoxeroides) are invasive and represent a biosecurity risk Use/applicability Most New Zealand regional councils monitor macrophytes in a rather cursory way, as part of physical habitat assessments (Davies-Colley et al. 2012b). Unfortunately, these assessments typically do not provide enough information for ecological analyses (Matheson et al. 2012). The reason for the absence of more detailed and comprehensive protocols is that excessive macrophyte growths occur sparsely in most regions, because the conditions that promote them (unshaded, low-gradient, soft-bottomed streams that rarely experience scouring floods) are rare. In Auckland, however, such conditions are common. Currently no national protocols are available regarding measurement of macrophyte growth in streams and rivers (Matheson et al. 2012). However, Matheson et al. (2012) propose a method for calculating indices relevant to: a) the ecological and Technical aspects of integrating water quality science in freshwater and coastal environments 100

111 flood conveyance impacts; and b) the aesthetic and recreational impacts of macrophyte growth in streams. These are, respectively, the percentage of stream cross-sectional area or volume (CAV) and the percentage of stream surface area (SA) occupied by macrophytes of different species. These indices represent a development of the Macrophyte Channel Clogginess (MCC) index of Collier et al. (2007), which assesses the surface area occupied by different macrophyte growth forms. Although these indices are fully developed for use, they are yet to be adopted widely Critique/review of existing approaches for macrophytes management/guidelines There are currently no national nuisance macrophyte abundance guidelines available for streams and rivers (Matheson et al. 2012). Matheson et al. (2012) recommend a provisional guideline of 50% of channel cross-sectional area or volume (CAV) above which instream ecological condition, flow conveyance and recreation values may be impaired. In addition, they recommend a provisional guideline of 50% of channel water surface area to protect instream aesthetic and recreation values. They note that these provisional guidelines are not based on a large body of empirical data, and that information specific to local sites can be used to set local guidelines in preference to general guidelines. They conclude that further research linking macrophyte abundance levels to effects on key instream values is required to refine the guidelines. Little information exists regarding relationships between instream macrophyte abundance and detrimental impacts on human water uses, therefore guidelines for specific water uses are lacking (Matheson et al. 2012) Strengths Although the CAV, SA and MCC indices include spaces for entering species names, scores may be calculated without identifying species. The indices described here are intuitive and relevant to both ecological functions and human values Limitations Information regarding the relationships between macrophyte CAV and ecological effects, e.g., responses of macroinvertebrate metrics, or thresholds of dissolved oxygen or ph at which fish may be harmed. The same is true for relationships with human uses and interests such as recreation, water intakes and flood prevention (Matheson et al. 2012). Technical aspects of integrating water quality science in freshwater and coastal environments 101

112 10.4 Relevance/suitability for Auckland The CAV and SA indices of Matheson et al. (2012) are relevant to Auckland streams, where macrophyte proliferations are not uncommon. The indices are constructed in a way that is suitable for Auckland streams Recommendations We recommend using the CAV index of Matheson et al. (2012) for assessing macrophytes as both indicators and agents of stream degradation for ecosystem health and flow conveyance. Likewise, we recommend using the SA index (Matheson et al. 2012) for measuring effects of macrophytes on human recreation and aesthetics. The suitability of these indices for development of management bands can be investigated to provide a measure of ecosystem health for macrophyte communities together with other water quality attributes/parameters. The provisional guidelines of Matheson et al. (2012) could be adopted in the interim, and refined if necessary by Auckland Council following application and in response to accumulated experience. This is because macrophytes have both positive and negative characteristics. They can be a major issue by choking rivers, reducing DO levels, reducing eel and other fish habitat and as a habitat for noxious weeds. They can also be seen as providing a positive service to rivers that would otherwise appear turbid, by trapping sediment, providing cover for fish, reducing temperatures and processing contaminants. Consequently, managing macrophytes by skilful shade planting is recommended, where the positive and negative factors are balanced, resulting in partial weed growth. This would require studies to determine optimum strategies. Technical aspects of integrating water quality science in freshwater and coastal environments 102

113 11 LakeSPI 11.1 Overview and importance LakeSPI is a management tool that uses Submerged Plant Indicators (SPI) for assessing the ecological condition of New Zealand lakes and for monitoring trends in lake ecological condition. It uses carefully selected features of submerged plant communities to assess the effects of catchment and water management on a lake and the impact of aquatic weed invasion in a lake. Its intended users are lake managers (Clayton et al. 2006a; Clayton et al. 2006b). LakeSPI was developed in the year 2000 to create two indicators: (1) change in the biodiversity condition of selected freshwater ecosystems and habitats compared with historic and current baselines, and (2) change in the distribution and abundance of selected plant pests (Clayton et al. 2006a). LakeSPI is comprised of three component indices (Table 11-1, Figure 11-1; de Winton et al. 2012). Table 11-1 Definition of measures contributing to LakeSPI index (de Winton et al. 2012). Index Factors measured Native Condition Index (NCI) This captures the native character of vegetation in a lake based on diversity and quality of indigenous plant communities. A high native condition index value will represent better lake condition. Invasive Condition Index (ICI) or Invasive Impact Index (III) This captures the invasive character of vegetation in a lake based on the degree of impact by invasive weed species. A high invasive condition index value will represent poorer lake condition. LakeSPI Index (LSI) This is a synthesis of components from both the native condition and invasive condition of a lake and provides an overall indication of a lake s ecological condition. Lake comparisons LakeSPI assesses and calculates LakeSPI indices based on a maximum potential score for each lake. This allows dissimilar lakes to be compared more appropriately. LakeSPI is based on SCUBA survey of submerged aquatic plants in lakes (de Winton et al. 2012). The recommended approach involves surveying at least five sites in each lake that supports representative vegetation cover exceeding 10% per 2 m 2. Lakes that do not exceed this threshold are termed non-vegetated, and cannot be scored. At each site, scuba divers score 11 metrics over a transect from shore to the deepest vegetation limit. Five of these contribute to the Native Condition Technical aspects of integrating water quality science in freshwater and coastal environments 103

114 Index NCI), five to the Invasive Impact Index (III) and one to the LakeSPI Index (Figure 11-1). Metrics for invasive weed development include an a priori ranking of 11 alien species according to severity of impact and habitat tolerances in New Zealand (de Winton et al. 2012). This metric, termed invasive species impact, scores 0 if no weeds are present and up to 7 for the highest ranked (most invasive) weed, Ceratophyllum demersum. If more than one invasive species is present, the higher score is allocated. Normalising indices for lake depth and expressing results as % of pre-european condition (i.e., maximum potential score) means shallow lakes where vegetation maximum depth is constrained by lake bathymetry are not unduly penalised relative to other lakes. Figure 11-1 LakeSPI components, showing 11 metrics (with their score ranges) contributing to three indices. Note scores for invasive impact metrics are reversed before contributing to the LSI, while summed metrics for the Native Condition Index and the LSI are normalised as a percentage of the expected pre-european condition. LakeSPI is considered complementary of water quality monitoring in lakes (Davies- Colley et al. 2012a). In the study of de Winton et al. (2012), III metrics were not significantly related to TLI, or landscape scale surrogates for anthropogenic pressure (e.g., pasture cover), indicating the process of weed invasion to be largely decoupled from eutrophication and other land use pressures. NCI metrics measuring Technical aspects of integrating water quality science in freshwater and coastal environments 104

115 native condition were strongly negatively related to increasing eutrophy, however, they were also influenced by invasive weeds. In a comparison of 112 lakes across New Zealand (Verburg et al. 2010), overall LakeSPI scores were only moderately correlated with TLI scores (r=0.54). The combination of metrics within LakeSPI can capture and differentiate a wide range in ecological condition of lakes, and when integrated within LakeSPI indices (LSI, NCI and III), it provides the means to report and compare ecological condition between lakes (de Winton et al. 2012). LakeSPI is an established index for monitoring lakes across New Zealand. It has been applied to over 200 lakes, and was one of two indices used for a major report regarding the state and trend of New Zealand lakes in 2010 (Verburg et al. 2010). LakeSPI was recommended for adoption by all regional councils and unitary authorities across New Zealand in the National Environmental Monitoring and Reporting (NEMaR) consultation (Hudson 2011) Use/applicability LakeSPI is designed for assessing, monitoring and reporting on lake ecological condition. LakeSPI scores can be used to: Monitor trends over time within a single lake. Assess or compare the ecological condition of lakes across a region or across the country. Rank the state of lakes in their region and thereby prioritise those most in need of protection, surveillance or management. Contribute directly to reporting of lake environmental trends at the local, regional and national levels. Make comparisons between dissimilar lakes, e.g., those of different depths and from different regions. Help assess the effectiveness of catchment and lake management initiatives. The LakeSPI method can also be applied to historic vegetation survey data for assessing retrospective lake condition changes (Clayton et al. 2006a). The LakeSPI method is suitable for use in all lakes apart from those where submerged plant cover is less than ten percent or where environmental conditions (e.g., salinity, acidity, altitude or restrictive optical properties) prevent the development of typical submerged vegetation (Clayton et al. 2006a). Technical aspects of integrating water quality science in freshwater and coastal environments 105

116 The LakeSPI method is suitable only for freshwater lakes. It is not suitable for brackish or estuarine waterbodies, since the plant species tolerant to saline conditions are quite different to those found in fresh water. The LakeSPI method will also not work effectively in any lake where the ph or dissolved chemicals affect the presence of a normal complement of submerged plant types. For example, the Kai- Iwi lakes in Northland have low alkalinity that only supports charophyte vegetation. To date, over 200 lakes across New Zealand have been surveyed or scored for LakeSPI. The results of these surveys, and the underlying survey information, are stored on a website that has a user-friendly user interface for viewing results ( Critique/review of LakeSPI approach to lake management Condition bands for LakeSPI are well developed, and include five categories: Excellent (>75% of maximum potential score), High (50-75%), Moderate (20-50%), Poor (0-20%) and Non-vegetated. A large dataset (derived from more than 200 lakes) is available at these data may be used to compare the score of a new site Strengths Submerged plants integrate a range of environmental conditions that affect plant growth. In particular, LakeSPI is sensitive to two key factors that influence all water bodies throughout New Zealand, and that managers generally aim to regulate or minimise. These factors are: (1) the effect of catchment developments that result in increased sediment and nutrient influx to receiving water bodies; and (2) the impacts arising from invasive water plants (Clayton et al. 2006a). The LakeSPI method focuses on the littoral zone (margins) of lakes, whereas physico-chemical water quality monitoring is usually done in open water near the lake centre. In lakes where the littoral zone represents a large proportion of the lake area, the water quality and ecological condition occurring within the littoral zone can be very different to the open water or centre lake condition. The littoral zone is very important to the overall ecological state of many lakes, and it is where public interaction and interest are greatest. Therefore, it is important to focus attention on the ecological well-being and biological functioning of the littoral zone where submerged plants tend to dominate. LakeSPI scores are expressed as a percentage of the maximum potential score, allowing lakes of different types (specifically, different depths) to be compared. The LakeSPI method is rapid enough to enable assessment of a single lake in a day. For monitoring purposes, a sampling frequency of once in 1-3 years is sufficient because macrophytes are relatively long-lived and integrate conditions at this time Technical aspects of integrating water quality science in freshwater and coastal environments 106

117 scale. This is in contrast to physic-chemical water quality variables that must be sampled frequently (e.g., monthly) to capture seasonal and climatic cycles Limitations Not all lakes can be assessed using the LakeSPI method. The lake must have submerged plants and cover of vegetated areas must exceed ten percent before the scoring system will work. Below this threshold, lakes are simply classed as nonvegetated. Forty percent of Auckland lakes surveyed to date are classed as nonvegetated (lakespi.niwa.co.nz). Some lakes may be unsuitable for the LakeSPI method due to their vegetation type. Any lake with emergent species around the lake margins must also have submerged vegetation present for scoring purposes. Many quite small lakes (such as farm ponds and reservoirs) are surrounded by emergent vegetation (e.g., raupo (Typha)) with their surface waters often covered by free-floating plants (e.g., duckweed (Lemna), water fern (Azolla)), or bottom rooted plants with large surface floating leaves (e.g., water lilies (Nymphaea species)). Dense mats of floating plants will often exclude light and prevent submerged species from growing, so these types of lakes would be unsuitable. LakeSPI will pick up new invasive species if they are already well established and having an impact on lake condition, but it is not a method designed to pick up early stages of any new invasive species establishment. A site targeted surveillance method is required for this purpose, where sites vulnerable to weed incursions, such as public access points are targeted. LakeSPI requires special expertise, thus most regional councils will probably require an outside agency such as NIWA to do their LakeSPI monitoring (Davies-Colley et al. 2012b) although that may change in future (Mary de Winton, NIWA, pers. comm.). This means an individual LakeSPI survey is relatively expensive. However, because surveys are required relatively infrequently, LakeSPI is still regarded as a costeffective monitoring tool relative to other monitoring tools Overall Increased sediment and nutrients from catchment activities, and displacement of native vegetation by invasive alien plant species are major influences on lake ecology and condition. The submerged plant indicators used in LakeSPI provide an effective means of categorising the extent of these impacts (Clayton and Edwards 2006). Although individual surveys are relatively expensive, LakeSPI surveys are required only every 1-3 years, therefore the long-term cost of LakeSPI monitoring is lower than for water quality monitoring, which requires monthly boat trips to open water Technical aspects of integrating water quality science in freshwater and coastal environments 107

118 areas. Thus, for the same cost, more lakes can be surveyed with LakeSPI than with traditional water quality monitoring techniques (Clayton et al. 2006a) Relevance/suitability for Auckland LakeSPI is suitable for and has been applied widely in the Auckland region. Of the >200 lakes surveyed nationwide, 25 lakes are in the Auckland region, from Spectacle Lake near Mangawhai to Parkinson s Lake near Waiuku. An issue in Auckland, however, appears to be a higher than average number of nonvegetated lakes. Ten of the 25 Auckland lakes surveyed to date are classed as Nonvegetated ( meaning that LakeSPI is not a useful tool for assessing their ecological condition (Table 11-2). Table 11-2 LakeSPI data and last monitoring date for Auckland lakes (from: Recommendations 1. LakeSPI is recommended as a simple, cost-effective method for monitoring the ecological condition of lakes. It is suitable for development of management bands to provide a measure of ecosystem health for lake macrophyte communities together with other water quality attributes/parameters. Technical aspects of integrating water quality science in freshwater and coastal environments 108

119 2. Because LakeSPI responds to somewhat different environmental conditions than other lake indices such as the Lake TLI, and focuses on the littoral zone rather than the open water environment, it should complement, rather than replace, physico-chemical monitoring of lakes. 3. LakeSPI is recommended every 1-3 years for lakes where change is expected, or risk of invasion is high, but can be relaxed to intervals of 10 years or so for lakes that are considered stable (Clayton et al. 2006a; Davies- Colley et al. 2012a). Technical aspects of integrating water quality science in freshwater and coastal environments 109

120 12 Fish IBI 12.1 Overview and importance Significant social, cultural and economic values are placed on the fish populations of New Zealand s streams and rivers, not only for their intrinsic biodiversity value, but also importantly as supporting the whitebait, eel and trout fisheries, and as a traditional food source for Maori (Storey 2013). Monitoring of fish is important because of the values associated with them. Fish, like benthic macroinvertebrates, are sensitive to many of the aspects of river environments, and because they are high in the food chain, they are affected indirectly by the impacts on other aquatic biota (Barbour et al. 1999). In addition, fish are severely affected by three other common human impacts that do not greatly affect macro-invertebrates: (i) artificial barriers, such as culverts weirs or low water clarity, that block migration between rivers and the sea, may reduce the presence and abundance of migratory fish species in upstream river reaches (Boubée et al. 1997; Rowe et al. 1998); (ii) native fish are also affected by the presence of introduced fish species, which may prey on certain native species and/or compete with them for food (McDowall 2003); and (iii) commercial, recreational and customary (mahinga kai) harvests may significantly affect fish populations in river and lake environments. Monitoring fish richness and abundance shows the presence and severity of each of these human-induced impacts, which will not be indicated by monitoring of other biological groups. In addition, due to their long life cycles, fish indicate river health over comparatively long temporal scales relative to invertebrates. For these reasons, fish monitoring has been recommended for regional council SoE monitoring programmes (Davies-Colley et al. 2011). The Fish Index of Biological Integrity (IBI) (Joy et al. 2004) is designed to be a biological indicator of stream condition, correlated with habitat and water quality degradation. It was developed from fish presence/absence data from sites across New Zealand held in the NZ Freshwater Fish Database. The Fish IBI is multimetric, based on six component indicators of fish community integrity. The metrics chosen were derived or adapted from similar indices developed overseas. For the New Zealand IBI, metrics were modified or removed to enable the index to reflect the unique attributes of New Zealand stream fish assemblages (Joy et al. 2004). The six metrics are: (1) the number of native species (2) the number of native riffle-dwelling species Technical aspects of integrating water quality science in freshwater and coastal environments 110

121 (3) the number of native benthic pool species (4) the number of native pelagic species (5) the number of intolerant or sensitive native species, and (6) the proportion of alien species. The first five metrics above are scaled in relation to Maximum Species Richness Lines, which are a function of altitude and distance to coast. These metrics are summed along with metric 6 to give overall Fish IBI score. The IBI score varies from a minimum of 0 to a maximum of 60. The metrics are believed to describe the changes that occur in fish assemblages as an ecosystem becomes impaired (Table 12-1). Thus, the overall Fish IBI score is reduced by reduced physical habitat complexity, degraded water quality (including increased temperature, suspended sediment, ammonia), migration barriers, and introduced species. Introduced species both represent an ecological impact themselves, and are believed to indicate more degraded habitat conditions (as they are typically more tolerant of a degraded environment than native species). Testing of the Fish IBI has confirmed that Fish IBI scores are correlated with upstream land use (Joy 2009; Joy et al. 2004). In these studies, high IBI scores were associated with high proportions of catchments in native forest, whereas high levels of agriculture and moderate to high levels of urbanisation were associated with low IBI scores. However, some natural factors that cannot be included in the IBI approach (such as geology and temperature) also influence fish assemblages. Therefore, index scores need to be interpreted carefully. Table 12-1 A summary of the expected changes in fish community structure with declining environmental conditions, and the metrics that capture these. Effect on fish assemblage of declining environmental conditions Metric (i) Reduction in the number of native species 1, 6 (ii) Reduction in the number of intolerant (sensitive) species 5 (iii) Reduction in the number of species in specific habitats 2,3,4 (iv) Increase in the number of exotic species 6 The Fish IBI has been widely used by regional councils for SoE reporting. It has also been used for national-scale analyses of fish community trends and responses to land cover changes (Joy 2009). Technical aspects of integrating water quality science in freshwater and coastal environments 111

122 The Fish Quantile IBI, a recent modification to the Fish IBI, is the use of quantile regression to fit the Maximum Species Richness Lines (Joy 2009). This modification is believed to make site scores more accurate, as the Maximum Species Richness Lines are fitted statistically rather than by eye. However, for many sites the modification also makes scores higher relative to the previous IBI system (Joy 2009) Use/applicability A Fish IBI score can be calculated from a single site survey using any standard fish sampling method (Joy et al. 2013). The score is likely to vary according to the sampling method used, as each sampling method has biases that affect the likelihood of catching different fish species. However, because the Fish IBI is based on species presence/absence, it is less sensitive to these biases than if it were based on abundances. The Fish IBI is intended for use in streams and rivers only, not lakes (Joy et al. 2004) Critique/review of Fish IBI approach to managing freshwater ecosystems As a guide to interpreting the final scores, Joy and Death (2004) give the following condition bands for IBI scores: low quality (IBI=1 20), medium quality (IBI=20 40), high quality (IBI=40 60), and sites where no native fish were caught (IBI=0) Strengths IBI overcomes the difficulty that fish species richness declines with altitude and distance from coast, which makes comparison of sites difficult. The Fish IBI scales the richness metrics of a site by its maximum possible richness using the site s altitude and distance from coast. The IBI of reference sites (where human influences remain minimal) appears to be relatively stable over time (Joy and Death 2004). At sites experiencing minimal change in human impacts, more than 80% of repeat samples were within six IBI points of each other, even over relatively long time scales Limitations The current version of the Fish IBI is based on species presence/absence only. However, significant impacts on fish communities may cause decline in abundance, but not total loss of, a species. For example, a new structure may prevent migration during most flow conditions, but occasionally a few individuals may pass, maintaining the presence of this species. Also, many sites have both eel species present regardless of catchment land use, but the relative abundance of the two species differs dramatically between pasture and native forest streams. Total loss of a Technical aspects of integrating water quality science in freshwater and coastal environments 112

123 species usually only results from major degradation of a site. Although the Fish IBI does not capture changes in abundance, no other available metric captures these either. New fish sampling protocols (which are being adopted by regional councils for SoE monitoring) gather abundance data, and Joy (2013) proposes an update of the Fish IBI to incorporate abundance. In a trial, this updated IBI showed greater power than the old version to discriminate between pasture-dominated and native forestdominated streams. However, this version is not yet available. Fish age/size data contain much information that help to diagnose particular environmental stressors. For example, the absence of young fish may indicate that a new migration barrier has appeared, whereas the absence of large fish may indicate overfishing pressure. This information is not captured in the current Fish IBI, but no alternative metric captures it either. Updates proposed to the Fish IBI would incorporate size information (Joy 2013). Different fishing methods are required for different types of stream (Joy et al. 2013). These methods differ in their effectiveness for catching different fish species, producing different IBI results. The Electro-fishing method (EFM) gives the highest IBI readings as it is the least selective method (Joy and Death 2004), but it is not possible to use EFM in all stream types (Joy et al. 2013). Fish catchability also varies both spatially and temporally, though this problem can be reduced by consistently sampling at the same time of year (Joy et al. 2013). Fish monitoring is expensive in terms of time (1-8 hours per site) and equipment, and requires specialist skills for collecting and identifying fish and reporting the results (Davies-Colley et al. 2011). Auckland Council routinely monitors fish as part of its SoE monitoring programme, so these requirements should not pose an obstacle Overall Although IBI scores are correlated with gradients of land use intensity, other natural environmental factors also strongly influence IBI results. In a survey of 5497 sites across New Zealand (Joy and Death 2004; Figure 12-1), sites with high IBI scores were associated with high proportions of the catchment in native forest whereas sites with low IBI scores were associated with high proportions of the catchment in farming and urban land use. However, geology (greywacke vs. sand/schist), mean air temperature and evaporation were also strongly correlated with the gradient from low to high IBI score. Sites with no fish do not appear to lie on the same gradient as low-medium-high IBI scores, and were associated primarily with increasing distance from the coast (Figure 12-1). Therefore, it appears that an IBI of zero should not necessarily be considered as an extreme low score. Technical aspects of integrating water quality science in freshwater and coastal environments 113

124 Figure 12-1 Position of average values of the four IBI condition band classes, in relation to key environmental variables. The position of the IBI class averages and biplot arrows were obtained using linear discriminant analysis on 51 environmental variables. The arrows show correlations between environmental variables and the axes of the plot. Data were drawn from 5497 New Zealand fish survey sites (Joy et al. 2004). A closer look at the relationship between IBI condition bands and intensity of different catchment land uses is shown in Figure 12-2 (from Joy and Death 2004). The mean IBI score increased with increasing catchment proportions of native forest, and decreased with increasing proportions of catchments in farming, urban land use and exotic forestry. It is important to note that the relationships were not linear, with a low threshold for % urban land use, and higher thresholds for farming and exotic forestry land uses. Technical aspects of integrating water quality science in freshwater and coastal environments 114

125 Figure 12-2 Mean IBI scores and standard errors for watershed proportions [low (<33%), medium (33 67%), and high (>67 %)] of different land-use categories for 5497 sites in New Zealand from the New Zealand freshwater fish database. Bars with different letters are significantly different (P <0.05); the number in the bar denotes the number of sites in each category. Overall, the Fish IBI was recommended in the NEMaR process (Hudson 2011) as the best tool currently available for summarising fish data. Schallenberg et al. (2011) also recommend it as a measure of ecosystem pristineness. Technical aspects of integrating water quality science in freshwater and coastal environments 115

126 12.4 Relevance/suitability for Auckland The model underlying the Fish IBI must be adapted for each region of New Zealand. An Auckland Fish IBI has been developed and is already incorporated into the SEV. Because Auckland Council reports SEV results for its SoE reporting every two years, it can be assumed that fish surveys are conducted and that Fish IBI scores are calculated, every two years from all 82 SoE sites. Auckland streams are all relatively low in altitude and close to the coast. In addition, no endemic species with distributions restricted by evolutionary factors exist in Auckland. Therefore, the Fish IBI should perform as well in Auckland as in any region Recommendations The Fish IBI is recommended as the best available index for assessing the ecological integrity of the fish community. The quantile version of the Fish IBI (Fish QIBI) is believed to be more accurate than the non-quantile version, but care must be taken not to mix results between the two methods, as the Fish QIBI produces higher values than the Fish IBI. The factors impacting on fish communities tend to occur at catchment rather than site scales. Therefore, instead of reporting Fish IBI scores by individual site, it may be more appropriate to combine them from all sites in a catchment into a single catchment-scale score. Alternatively, it may be better to use an index that uses catchment scale data directly (e.g., SIFR, described below). Sampling should only take place in late summer, as this is when maximum species diversity occurs in New Zealand streams because all diadromous species are present in fresh water (McDowall 1990). The full range of habitat types present at a site should be sampled Alternative indices Alternative indices have been developed in New Zealand that may compliment Fish IBI. These are reviewed here for convenience, but are not recommended as potential replacements for Fish IBI SIFR (Status Index for Fish in Rivers) The factors impacting on fish communities tend to occur at catchment rather than site scales, reducing the occurrence of vulnerable species at affected sites. SIFR (Status Index for Fish in Rivers, Rowe 2013) acknowledges this by directly measuring the diversity of the riverine fish community at a river-basin scale. It summarises the overall frequency distribution for the number of species per site, using data from multiple sites throughout a river basin. Technical aspects of integrating water quality science in freshwater and coastal environments 116

127 The frequency distribution of native species richness at sites within a catchment is highly skewed, with most sites having a low richness (<=2 species), but a few having high numbers (up to 12 species). To account for this skewness, a weighted mean is used instead of an unweighted mean to better reflect the status of a fish community in a catchment. SIFR is calculated as follows, where fn is the frequency of sites containing n species of fish, and n is the maximum number of species at a site: SIFR = 1 f1 + 2 f2 + 3 f3 + 4 f4 +..N fn SIFR reflects the effects of physical stressors affecting connectivity and habitat, as well as biotic stressors such as invasive species. In a study of 82 rivers throughout New Zealand (Rowe 2013) low SIFR values (<2.5) characterised rivers with reduced connectivity, loss of forest cover, high levels of sedimentation, poor water quality and/or urban development. The least degraded rivers all had values > 4.0. SIFR is particularly sensitive to the occurrence of trout, with values decreasing linearly with increasing trout occurrence from a mean of 3.1 where trout were absent down to a mean of 1.9 in rivers completely dominated by trout. Guidelines: Rowe (2013) compares SIFR values between rivers known to be degraded with those known to be relatively pristine in order to determine useful thresholds and benchmarks for classifying rivers. However, he does not provide numeric values for these thresholds. Strengths: SIFR has advantages in being simple to calculate and based on presence/absence data (which require less intensive sampling than abundance estimates). It provides managers with a tool for assessing the overall effects of a range of river restoration works on river ecology and fish community status while simultaneously providing key stakeholders (i.e., Māori, fishery managers, conservation authorities, commercial fishermen, angling organisations) with an ecological measure relevant to their main interest in river restoration. Limitations: SIFR values are sensitive to the altitudinal distribution of sample sites within a river basin, being lower especially where a large proportion of the catchment is more than 200 m a.s.l. However, this effect can be detected and corrected for, either by a correction factor standardising the raw values of SIFR for differences in the altitudinal distribution of sampled sites, or by more widespread sampling, which ensures an equitable spread of sample sites is taken throughout a river basin. SIFR is newly developed and is yet to be adopted by any regional council for fish monitoring or reporting. Overall: SIFR provides a measure of fish community biodiversity at a river basin scale that is related to the overall extent of degradation and the impact of multiple stressors within the constituent catchments of this river. Technical aspects of integrating water quality science in freshwater and coastal environments 117

128 Observed/expected models A predictive model that allows an observed/expected ratio to be calculated is recommended by Joy (2013). However, developing such a model would require data from up to 200 reference sites, which would take a large amount of sampling effort, presuming this large number of sites could be located. Leathwick et al. (2005) produced a model predicting the probability of occurrence of individual fish species for every reach of the River Environment Classification across New Zealand. This model might appear to provide the expected fish community against which an observed community could be compared. However, Leathwick et als model predicts the community present given all current human pressures and impacts on stream ecosystems. In contrast, the expected community required for an observed/expected model is that expected in the absence of human pressures. Therefore, while Leathwick et als model provides a valuable context for future conservation management in New Zealand's rivers and streams, it is not suitable as a monitoring tool. Technical aspects of integrating water quality science in freshwater and coastal environments 118

129 13 Lake Trophic Level Index (TLI) 13.1 Overview and importance The Lake Trophic Level Index (TLI) is a measure of the trophic state of a lake. Trophic state has been defined as the life-supporting capacity per unit volume of a lake (Burns et al. 2000). Six commonly measured variables are widely accepted as good indicators of the trophic level of a lake: Chlorophyll a (Chl a), which is a measure of the density of phytoplankton (single-celled algae) in the water. Secchi depth (SD), which is a measure of the visual clarity of the water. Total phosphorus (TP). Phosphorus is a major nutrient affecting growth of phytoplankton. Total phosphorus includes organic and inorganic forms of phosphorus, both particulate and dissolved. Total nitrogen (TN). Nitrogen is another major nutrient affecting growth of phytoplankton. Total nitrogen includes organic and inorganic forms of nitrogen, both particulate and dissolved. Hypolimnetic volumetric oxygen depletion rate (HVOD), which is the rate at which oxygen is consumed in the bottom waters of lakes. It is driven by decomposition of organic matter. Phytoplankton species and biomass. The TLI, developed and described by Burns et al. (2000; 1999), combines the first four of these indicators (Chl a, SD, TP and TN) into a single number, and uses that number to locate a lake on a scale of eutrophy from Ultra-microtrophic (low TLI) to Hypertrophic (high TLI). The individual indicators are logarithmically transformed and scaled so that each is on the same scale and contributed equally to the TLI. The full TLI is sometimes called TLI4 as it comprises four indicators. A slightly simpler form, TLI3, omits Secchi depth. TLI3 may be used to allow comparison between a larger number of lakes, because there are a number of monitored lakes for which there are no Secchi depth data, and in other lakes Secchi depth is controlled mainly by sediments or coloured organic matter, which are not related to trophic state. Experience has shown that excluding Secchi depth makes little difference to overall TLI scores and TLI3 is very strongly correlated with TLI4 (Verburg et al. 2010). In theory, TLI values range from 0 (Ultra-microtrophic) to 7.0 (hypertrophic); in practice, for 112 lakes monitored across New Zealand, TLI ranged from 1.4 to 7.1 (Verburg et al. 2010). Technical aspects of integrating water quality science in freshwater and coastal environments 119

130 The TLI has been used extensively for reporting lake water quality in New Zealand. It was one of two indices used in a 2010 national report on the state and trend of lake water quality in New Zealand (Verburg et al. 2010). It was strongly endorsed in NEMaR reports (Davies-Colley et al. 2012a) for nationally consistent State of the Environment reporting Use/applicability The TLI was developed for NZ and is suitable for a wide range of New Zealand conditions (Burns et al. 2000). For lakes where turbidity is high because of frequent sediment re-suspension (e.g., shallow lakes), water clarity as measured by Secchi disk depth may not reflect algal biomass, and therefore trophic state, very well. In such lakes, one option is to modify TLI by a correction factor using measured non-volatile suspended solids (NVSS), which accounts for the proportion of turbidity not related to algal biomass. Alternatively, Secchi disk depth may be omitted from the TLI calculation, i.e., TLI3 can be used instead of TLI4 (Davies-Colley et al. 2012a). Shallow lakes, which are subject to rapid change, must be monitored monthly. Indeed, in all lakes, monthly monitoring is highly desirable for robust trend analysis and detection (Davies-Colley et al. 2012a). The TLI was developed exclusively for freshwater lakes and is not suitable for rivers, wetlands or brackish or saline waters. An estuarine TLI has been proposed, but is still in the conceptual stage Critique/review of TLI approach to lake management/guidelines Trophic state classes, based on the range of possible TLI values, are well-defined (Table 11-1; Burns et al. 2000). However, the trophic classes in Table 13-1 do not equate exactly to levels of human-induced eutrophication, since to some extent trophic state varies naturally among lakes. For example, lake depth, altitude, source of water and geographic region all affect TLI indicators (Verburg et al. 2010). Nevertheless, the trophic classes indicate modified conditions. In the survey by Verburg et al. (2010), lakes in catchments dominated by native forest were typically oligotrophic, whereas 84% of lakes in catchments dominated by pastoral land cover were mesotrophic to hypertrophic. TLI3 was correlated with the proportion of pasture in a catchment (r=0.52, p< ) but not with the proportion of urban area (r=0.14, p>0.05) or proportion of exotic forest land cover (r=0.12, p>0.05). Verburg (2012) proposed objective bands (Excellent, Fair, Poor and Unacceptable) for six classes of lake. Lake classification is based on stratification (seasonal vs. polymictic), clarity, altitude and salinity (fresh vs. brackish). The objective bands do Technical aspects of integrating water quality science in freshwater and coastal environments 120

131 not refer specifically to TLI values, but are based on values of the TLI component variables (Chl a, Secchi depth, TP and TN), therefore they seem applicable to TLI. Table 13-1 Trophic level categories related to ranges of TLI scores and their component indicator scores (from Burns et al. 2000). Abbreviations: Chl a = Chlorophyll a; TP = total phosphorus; TN = total nitrogen. Trophic state Trophic level Chl a Secchi depth TP TN classes (TLI) score (mg m -3 ) (m) (mg m -3 ) (mg m -3 ) Ultra-microtrophic Microtrophic Oligotrophic Mesotrophic Eutrophic Supertrophic Hypertrophic >31 <0.4 >96 > Strengths Although lakes vary naturally to some extent with regard to trophic state, the TLI correlates well with catchment land use (Verburg et al. 2010). A trophic state of mesotrophic or higher usually indicates human-induced eutrophication, typically due to production land use in the lake catchment (Verburg et al. 2010). There was no correlation with proportion of urban (r=0.14) or exotic forest (r=0.12) land cover in the catchment. The NEMaR expert panel agreed that the TLI (or a TLI modified to function in polymictic, glacial flour or peat-stained lakes) was suitable for national reporting purposes, particularly if changes in TLI rather than the absolute TLI value were considered (Hudson et al. 2012). The TLI has been used extensively for reporting lake water quality in New Zealand Limitations The trophic level index (TLI) is affected by natural variability in turbidity, which reduces Secchi depth. Factors such as glacial flour or (more relevant to Auckland) suspension of bottom mud by wind disturbance may lower TLI, even though they are unrelated to algal density or trophic state (Hudson et al. 2012). Technical aspects of integrating water quality science in freshwater and coastal environments 121

132 The TLI score may not accurately reflect the trophic state of a lake that is highly enriched with one nutrient, e.g., nitrogen. A solution is to report the TLI components as well as the single TLI score (Hudson et al. 2012). TLI is a measure of biomass, not lake productivity, since Chlorophyll a is a measure of algal standing stock, rather than algal productivity (Hudson et al. 2012). Technical errors can occur in calculating average TLI values over time. For example, if raw data for the component variables are averaged over a year before being combined to calculate an annual value of TLI, results may be biased by up to 10% due to skewness in the time-series data (Davies-Colley et al. 2012b). The correct method is to first combine all the component variables on each date into a TLI score, then average these TLI scores over a year. Monitoring TLI is relatively costly because accurate estimates require monthly sampling from a boat. Adding NVSS to sampling efforts to correct for natural turbidity differences increases the cost Relevance/suitability for Auckland TLI has been used for routine monitoring of lakes across New Zealand, including Auckland, for a number of years. Therefore it is considered suitable for Auckland Recommendations TLI is recommended as suitable for assessing the trophic state of freshwater lakes in Auckland. It is particularly robust for monitoring changes in trophic state in individual lakes over time. For assessing lake health in terms of human impact, the condition bands of Verburg (2012) may be more appropriate than a direct interpretation of TLI trophic classes, since to some extent trophic state varies naturally among lakes. Verburg s (2012) system involves classifying lakes before assigning them to condition bands. We adopt the recommendation in NEMaR (Davies-Colley et al. 2012b) of monthly determination of TLI, because many Auckland lakes are shallow and hence subject to rapid change, and because trend analysis requires a high frequency of sampling. Thus, sampling should be postponed but not cancelled in bad weather. To calculate the mean TLI for a lake over a time period (e.g., one year), the TLI should be calculated for each sampling event, and the individual TLI values averaged over the period (Davies-Colley et al. 2012b). The scores of the component indicators (Chl a, SD, TP, TN) should be reported in addition to the single TLI score. Technical aspects of integrating water quality science in freshwater and coastal environments 122

133 14 CCME Water Quality Index 14.1 Overview and Importance Indices are communication and education tools that summarize a number of water, sediment and soil quality variables into a single measure of overall water, sediment or soil quality. Indices are not intended to replace detailed assessments of ecosystems. The Water Quality Index (WQI) is a tool that provides consistent procedures for Canadian jurisdictions to report water quality information to both management and the public (CCME 2001). The WQI was in part based on early New Zealand work aimed at providing simplified water quality indices related to various water uses (Smith 1990). More recently the single index approach has been reviewed for application in New Zealand as part of the national monitoring programme (Davies-Colley et al. 2012a; Hudson 2011). The Water Quality Index Calculator is an MS EXCEL workbook which contains macros. The spreadsheet can contain up to 400 water quality parameters which can be included in the WQI calculation. There are three parts to the CCME WQI: A technical report describing how the index was developed. A user's manual outlining how to use the index. A user-friendly program that calculates index values based on information input by the user, updated in Use/applicability/importance The Canadian WQI is not directly applicable to New Zealand freshwaters in its present form. An alternative WQI has been developed and applied to the river water quality data collected for SoE monitoring by the Auckland Council (Lockie et al. 2013) Critique/review of existing WQI approaches CCME WQI The CCME approach uses water quality results to produce four water quality indices, and these indices can be used to assign a water quality class to each monitoring site. The four indices are: Scope This represents the percentage of parameters that failed to meet the objective at least once during the time period under consideration (the lower this index, the better). Technical aspects of integrating water quality science in freshwater and coastal environments 123

134 Frequency This represents the percentage of all individual tests that failed to meet the objective during the time period under consideration (the lower this index, the better). Magnitude This represents the amount by which failed tests exceeded the objective (the lower this index, the better). This is based on the collective amount by which individual tests are out of compliance with the objectives and is scaled to be between 1 and 100. This is the most complex part of the index derivation and the reader is referred to CCME (2001) for full details. WQI This represents an overall water quality index based on a combination of the three indices described above. It is calculated thus: WQI = [{ (Scope 2 + Frequency 2 + Magnitude 2 )} 1.732] The divisor normalises the resultant values to a range between 0 and 100, where 0 represents the worst water quality and 100 represents the best water quality. The CCME WQI is highly flexible and is able to accommodate an extensive range of water quality variables, and to quantify deviation from a suite of guidelines international, regional, and/or site-specific guidelines, as applicable. The Canadian WQI contains the Canadian guidelines so application to New Zealand waters would require revision. Auckland Council WQI The following describes the basis of the Auckland Council WQI: The WQI index is used by Auckland Council to assign a water quality class to each site using the following ranges: Greater than 90 = excellent water quality. Between 70 and 90 = good water quality. Between 50 and 70 = fair water quality. Lower than 50 = poor water quality. The above indices are calculated for each site using data for seven water quality parameters (Table 14-1). The objectives against which the Auckland Council water quality data are tested are derived from the range observed at the three Auckland Council reference sites (Cascades Stream, Wairoa Tributary and West Hoe Stream) over the five years preceding the relevant report (i.e., data for the 2007 to 2011 period was used for the 2012 SoE report). Technical aspects of integrating water quality science in freshwater and coastal environments 124

135 The ranges at these reference sites are used as these are considered to represent the best achievable water quality in Auckland (Lockie et al. 2013). Therefore, the index represents the deviation from natural conditions in the Auckland Region, rather than indicating whether the water quality is suitable for a particular purpose. The objectives are based on the 98 th percentile of the data from reference sites in the programme collected between 2007 and Table 14-1 The seven water quality parameters, and their objectives, used to produce the Auckland Council s WQI (Lockie et al. 2013). Parameter Objectives Dissolved oxygen (% saturation) Between 74 and 120% ph Between 6.4 and 8.1 Turbidity Ammoniacal nitrogen Turbidity Less than 33 NTU Less than 0.06 mg N/L Temperature Less than 18 C Total phosphorus Total nitrogen Less than 0.09 mg P/L Less than 0.8 mg N/L The basis of the Auckland Council s WQI are the physico-chemical values which are statistically-derived from data from three reference sites. This approach is similar to the physico-chemical trigger values in the ANZECC (2000) guidelines, which use an 80 th percentile of the reference site water quality as the guideline value. Both the ANZECC physico-chemical trigger values and the Auckland Council WQI are based on a reference site approach, and therefore, do not provide a measure of adverse biological effects in the rivers (see section for discussion). Results of indices calculated in this way can be comparable at the local, regional and national level as long as a consistent approach is followed across spatial scales and the appropriate details are reported. Further development of the Auckland Council WQI should be based on either the reference site approach or the NOF standards Relevance/suitability for Auckland The Auckland Council WQI has been used for routine monitoring in Auckland, for a number of years. The CCME WQI could be developed for Auckland. Technical aspects of integrating water quality science in freshwater and coastal environments 125

136 14.5 Recommendations We recommend that Auckland Council maintains a watching brief on future developments of methods similar to the CCME WQI. Modifications to the existing method may be incorporated into the Auckland Council WQI to enhance SoE reporting. Future developments of the Auckland Council WQI could be based on either the reference site approach or the NOF standards it is essential that a consistent approach is followed and the appropriate details that underpin each method are also reported. Technical aspects of integrating water quality science in freshwater and coastal environments 126

137 15 Other Indices The brief specified a suite of parameters which are commonly used for management of freshwaters (Appendix A). These include a number of indices which are largely composite habitat or biological measures. As part of this review, we have identified a number of other indices which are relevant to freshwater environments. We have provided a brief description of these indices, comments on advantages and disadvantages and a qualitative assessment of likely usefulness in Appendix C. The indices which we considered a high priority to complement freshwater monitoring and assessment programmes are summarised in Table Technical aspects of integrating water quality science in freshwater and coastal environments 127

138 Table 15-1 Other indices which should be considered a high priority to complement freshwater monitoring and assessment programmes. Indicator type Indicator name Habitat Description Advantages Disadvantages Usefulness (1=very useful, 5=not useful) Macroinvertebrate Indices EPT richness streams The number of "taxa" (species or genera) of mayflies, stoneflies and caddisflies indicates stream health, as these groups are pollution-sensitive. Can be calculated from existing macroinvertebrate data none 1 low if MCI already being used Cost Feasibility Include or exclude? Main reason for including or excluding easy include Complements the Macroinvertebrate Community Index (MCI) Requires reference site? no References Davies-Colley et al. (2012a); Davies- Colley et al. (2012b) Macroinvertebrate Indices Macroinvertebrate Indices Physical Habitat %EPT abundance streams The proportion of the invertebrate community belonging to mayflies, Can be calculated from existing macroinvertebrate data, provided data stoneflies and caddisflies indicates the are quantitative health of the stream. Total richness streams The total number of stream invertebrate Can be calculated from existing "taxa" (species or genera) is a macroinvertebrate data measure of diversity, indicating the condition of a stream. Rapid Habitat Assessment (RHA) streams Nine physical habitat variables scored from 1 to 20 and summed to give a single site score for physical habitat quality. Rapid field method. No equipment or further analysis required. Likely to become a standard protocol. none 1 low if quantitative data available, otherwise high none 1 low if MCI already being used Subjective unless thorough training given. Method is still in draft form. Not yet adopted as a standard protocol. All RHA variables are included in the Stream Ecological Valuation. 1 low easy with training easy include Complements the Macroinvertebrate Community Index (MCI) easy include Complements the Macroinvertebrate Community Index (MCI) exclude Same variables already included in the Stream Ecological valuation (SEV) no no Davies-Colley et al. (2012a); Davies- Colley et al. (2012b) Davies-Colley et al. (2012a); Davies- Colley et al. (2012b) no Clapcott (2013) Water quality Temperature depth profile lakes Temperature recorded at regular intervals on a vertical lake profile. Water quality Oxygen depth profile lakes Dissolved oxygen recorded at regular intervals on a vertical lake profile. Combined indices Ecosystem Health Monitoring Programme (EHMP) Index streams The freshwater method combines 3 macroinvertebrate indices, 3 ecosystem processes indices, 1 nutrient cycling index, 3 fish indices and 6 physicochemical variables into 5 summary scores and an overall grade for a catchment. A separate method is used for estuarine/marine habitats. Together with oxygen and nutrients, characterises lake condition and provide an understanding of lake processes, seasonal variability and allow rapid change in lake condition to be detected. Little extra cost if nutrients etc. are being monitored. Together with temperature and nutrients, characterises lake condition and provide an understanding of lake processes, seasonal variability and allow rapid change in lake condition to be detected. Little extra cost if nutrients etc. are being monitored. Combines a wide variety of ecosystem health measures into a single grade that is easy to interpret. The underlying scores are available for those who want more detail. The index must be adaped to NZ. Some of the variables are expensive, require development and are not currently measured in Auckland. 1 medium (low if lakes already being monitored) 1 medium (low if lakes already being monitored) easy include Useful additonal info to characterise lake state and processes easy include Useful additonal info to characterise lake state and processes 1 high difficult future Needs further development in NZ no no Davies-Colley et al. (2012a) Davies-Colley et al. (2012a) yes Bunn et al. 2010; mhealthmonitoringprogram/home.aspx Cultural Health Cultural Health Index (CHI) streams CHI is made up of three components: site status (significance to Tangata Whenua), mahinga kai (food species present and their productivity, access to and use of site) and cultural stream health (quality of water and physical habitat). Assesses variables relevant to Maori. Adaptable to local values, uses and perspectives. Threatened species streams, lakes, groundwat ers Provides an assessment of threatened or endangered aquatic species. Particularly important for rare species or those which may not be assessed during standard monitoring techniques (e.g., freshwater mussels (kakahi, kaeo)). Important component for freshwater biodiversity management. Development needed for Auckland streams. unique? requires time include An index that engages Maori and is relevant to Maori values is important. no Tipa and Tierney (2003, 2006) 1 include no Grainger et al. (2013). Technical aspects of integrating water quality science in freshwater and coastal environments 128

139 16 Integrating Estuary and Freshwater Management 16.1 Introduction This section describes technical aspects of setting integrated objectives and limits that support uses and values across coastal and freshwater environments. It describes the similarities and differences in setting limits in estuaries/marine and freshwater inflows, which reflect the difference in flow-through systems compared with accumulating systems. We provide guidance on how to establish objectives and limits for freshwater and estuaries that are integrated across the two environments. To achieve this, we analyse the management process under the NPS-FM using an example scenario. An example is used because a theoretical approach is very difficult to develop, and such situations can only be dealt with on a case-by-case basis. Following the example, we list the potential for conflicts for each parameter when setting limits across freshwater and estuarine environments Geophysical differences Streams and rivers are largely one dimensional flow-through systems. Contaminants dissolved or suspended in the water column have relatively rapid transit times (usually at the velocity of the river or stream). Limits for streams and rivers are typically set for dissolved and for suspended matter concentrations for low flow conditions representing worst case for available dilution and for point source discharges. This also is partly a time consideration: low flow occurs most of the time, so plants, animals, and recreational users generally receive the greatest exposure from contaminants (attributes) during low flow, which generally occurs in the warm summer period. However, there are situations where the total concentration or load is important, and these situations are usually related to when excessive quantities of suspended particles are transported during flood events. High rainfall events cause sediment runoff from the catchment, resulting in turbid flows and material settling out on the river bed as deposited sediment. As a general rule, the larger the particle being transported down a reach of the river, the more time it spends settled on the stream bed. In other words, the transit time down a river increases with the size of the particles; molecules, colloids, clay-sized particles and larger organic particles are transported at water velocities; boulders are only moved by very large floods. If significant amounts of fine particulate (e.g., >fine silts) settle on the bed, and in this way impacts on the value of that water body, then the loads of contaminants Technical aspects of integrating water quality science in freshwater and coastal environments 129

140 transported during high flows are important, and limiting the total load is an important option for management. This applies to sediment itself, but it also can apply to any contaminants associated with, adsorbed onto, or occluded within, sediment particles. For example, river beds could be managed in terms of the concentration of contaminants (heavy metals, persistent organic pollutants) in the sediment. In this case, limits may be set based on metrics that determine contaminant concentrations in the sediment; which could include total loads, total concentrations, particulate concentrations, and/or concentrations within the suspended solids being transported down the river. Estuaries have lower energy; longer residence times, and hence allows fine particulate matter to settle. This may be enhanced by coagulation and flocculation of very fine particles because of the increase in salinity that occurs in the transition zone from freshwater to the estuary. Estuaries also have a number of other important characteristics. In Auckland, estuaries are generally much shallower than lakes, so their beds are interacting with overlying waters much more dynamically. This means that while particulate matter settles, it can also be re-suspended by tidal currents and wind/wave processes. These internal processes result in recycling of the contaminants within the estuary. Thus the total fraction becomes even more important than the dissolved fraction, because particulate matter may not only generate dissolved contaminants from biophysical and biochemical processes as in lakes, but also contribute directly to water quality by being re-suspended into the water column. Estuaries have at least two end members the freshwater and seawater inflows so there is a gradient of concentrations, salinity and mixing processes between these two end members. Auckland estuaries have relatively small catchments and hence low freshwater inflows, therefore the seawater tidal exchange provides significant dilution of the freshwater within the physical bounds of an enclosed estuary. The seawater end member may also an important source of attributes (e.g., nutrients), and this needs to be taken account, e.g., in setting nutrient limits. The salinity also strongly affects the chemistry of the water and hence the ph, speciation of metals and ammonia, and hence toxicity of these contaminants. Hence estuary processes greatly modify inflowing contaminants, and total concentration or loads are more important than the inflow of dissolved concentrations in the freshwater inputs. The dissolved fraction may still be important, but in this case the effective concentration will be derived from freshwater inflow, estuary processes and seawater inflows. Technical aspects of integrating water quality science in freshwater and coastal environments 130

141 In conclusion, setting limits in estuaries/marine and freshwater inflows can be similar for some measures of state (e.g., dissolved oxygen, ph). However, some differences occur for some key parameters because of the difference in flow-through systems compared with accumulating systems. Similar differences are also found between rivers and lakes. These differences occur for TSS, priority pollutants which are strongly associated with particulate matter - such as Zn, Cu, Pb, DDT, PAH, and possibly nutrients. Table 16-1 compares similarities and differences in choosing attributes for freshwaters and marine waters. Table 16-1 Similarities and differences in attributes across different freshwater and estuarine surface water body types. Similarity/difference Similar primary emphasis on water column Some differences - emphasis on bed in estuaries (and in lakes to some extent) Completely different metrics and/or ways of measurement Attributes DO, temperature, ph, nitrate, ammonia, microbiological standards, clarity, turbidity TSS, heavy metals, other priority pollutants (e.g., DDT), nutrients Salinity, periphyton growths, MCI, Fish IBI, Fish QIBI, CCME, Lake SPI, SEV 16.3 The NPS-FM The NPS-FM establishes a legal and policy framework for building a national limitsbased approach to freshwater management. The NPS-FM requires maintaining or improving overall water quality in a region, and safeguarding of the life-supporting capacity, ecosystem processes and indigenous species (including their associated ecosystems) of fresh water. Councils are required to have: set freshwater objectives by 2025 that reflect national and local values set flow, allocation and water quality limits to ensure freshwater objectives are achieved address over-allocation manage land use and water in an integrated way, and involve iwi and hapū in freshwater decision-making. Councils and communities can choose the timeframes to meet freshwater objectives and limits. Technical aspects of integrating water quality science in freshwater and coastal environments 131

142 The NPS-FM is currently at various stages of implementation around the country as regional councils give effect to their policies through regional plans. Three councils intend to implement the NPS-FM in their regional plans by the end of 2014, and the rest have programmes in place for implementing it over a longer time period. Estuaries are specifically excluded from consideration in the NPS-FM. Nonetheless, amendments to the NPS-FM require that connections between freshwater bodies and coastal water be given regard when setting limits for freshwater. There is also an argument that estuarine management will benefit from a limits-based management approach in the same way that freshwater is expected to benefit. We present the following analysis as though the estuary is actually going to be managed under the NPS-FM although, in fact, there is no requirement for them to be managed in this way. In taking this approach, we aim to show, in some detail, why the management of freshwater under the NPS-FM also requires consideration of estuaries (and vice versa since external catchment processes are often a major driver of estuarine conditions, though the legacy of internal processes may maintain degraded water and sediment quality and recovery periods may be very long). Understanding this is the key to integrating the management of freshwater and estuaries. In the following, we develop these arguments using an example because a totally theoretical approach is very difficult to develop. These examples are simplified in that they do not fully consider the compulsory NPS-FM attributes for freshwater (ecosystem health and secondary contact). Additionally, there will be other factors that affect the sensitivity of the complex estuarine environment. These include: mixing of the freshwater inflows; and flushing of the estuary which is included in the estuarine classification system (Hume et al. 2007b) Analysis of the limits-based management process under the NPS-FM STEP 1 Define Management Units The first step of the management process laid out in the NPS-FM is to define the freshwater management units. For the purposes of this analysis, we have chosen an example of two rivers draining to an estuary, which we have divided into three hypothetical management units. These are the North River (and its surrounding catchment, to be more accurate); the South River (and its surrounding catchment), and the New Estuary. Figure 16-1 shows the North River, South River and New Estuary management units. Technical aspects of integrating water quality science in freshwater and coastal environments 132

143 Figure 16-1 North River, South River and New Estuary management units. STEP 2 Agree on Values For each management unit, values must be agreed. These are the intrinsic qualities that we appreciate or benefit from, or the uses to which we put freshwater (or estuarine water, in the case of the New Estuary). Values are typically determined following engagement with all interests within a management unit. ECan s zone committees were established for this purpose; Greater Wellington Regional Council (GWRC) is establishing whaitua for the same purpose. Management of freshwater under the new NPS quite literally begins with values. For our example, the North River has one value that we will imagine stakeholders have agreed on pursuing (fishing); the South River has two values (swimming and whitebait); and the New Estuary has one (shellfish gathering). STEP 3 Identify Attributes For each value, there will be a number of attributes, which are the characteristics or properties that need to be managed ( achieved ) to provide for the value at hand. Figure 16-2 shows a hypothetical table that links values to attributes. A 1 in the table at the intersection of an attribute and a value indicates that the attribute is primary, meaning that it must be managed to provide for the associated value. An example of a primary attribute for the value swimming is E. coli. A 4 in the table at the intersection of any given attribute and value indicates that the attribute is Technical aspects of integrating water quality science in freshwater and coastal environments 133

144 irrelevant to the value. An example is the attribute dissolved oxygen for the value electricity generation (note that Section 2.10 includes a more comprehensive table rating the importance of attributes under various values). The table in Figure 16-2 identifies three primary attributes for the value fishing in the North River (dissolved oxygen, fish passage and sedimentation rate); two primary attributes for the value whitebait (water clarity and river-edge habitat) and two primary attributes for the value swimming (E. coli and water clarity) in the South River; and four primary attributes for the value shellfish gathering in the New Estuary (sedimentation rate, heavy metals, water clarity and E. coli). In the following, we will consider only primary attributes for the agreed values. Note that these attributes would be chosen by council/community after assessing the science which identifies the attributes that must be achieved to enable the identified values to be achieved. Also note that the table linking values and attributes is different for the estuary compared to for the rivers. Although this is largely because the range of values in freshwaters is different to that in the estuarine environment, a difference may also arise because for many attributes, mass loads are more relevant in the estuarine environment than in rivers. An example is sedimentation rate although this may also be a significant parameter for freshwater lakes. The same table is used for the North and South Rivers. In reality, any table linking attributes to values is likely to vary by physiographic type and location of the management unit. This also leads to an important conclusion: the integration of freshwater and estuarine water management will need to be tackled on a case-by-case basis. Technical aspects of integrating water quality science in freshwater and coastal environments 134

145 Figure 16-2 Hypothetical table linking values and attributes for the North River, South River and New Estuary. The primary attributes for each agreed value are highlighted. Scores: 1 = Highly useful and relevant; 2 = Moderately useful or relevant; 3 = Unlikely to be useful, poor relationship; 4 Not useful or relevant. Steps 4 7 are depicted in Figure 16-3, which connects values, attributes, objectives, limits and management actions. This figure shows where the National Objectives Framework (NOF) and other various guidelines, including the ANZECC guidelines, may be used in the management and decision-making process. The figure also shows where the integration of freshwater and estuary management sits. Technical aspects of integrating water quality science in freshwater and coastal environments 135

146 Figure 16-3 Steps 4 7 in the management process, connecting values, attributes, objectives, limits and management actions, showing the use of the NOF and guidelines, and showing where the process of integrating freshwater and estuary management sits. Technical aspects of integrating water quality science in freshwater and coastal environments 136

147 STEP 4 Developing Objectives At least one objective needs to be created per value. This process is shown in Figure 16-4, which is extracted from Figure Figure 16-4 Creating objectives for each value (green text). Where appropriate, an intermediate decision is made on what level or state of each attribute should be achieved, and that decision is then converted into an objective. This intermediate step will not be appropriate for every attribute. The NOF may be used to make the intermediate decision regarding attribute state, but other types of information may also be used. Here is an example intended to show how the NOF works: Technical aspects of integrating water quality science in the freshwater and coastal environments 137

148 For the value ecosystem health in rivers, the NOF identifies the attributes nitrate, ammonia, dissolved oxygen and periphyton (or slime). The NOF is saying here that these four things all have a bearing on ecosystem health, and so they must be managed in order to provide for that value. The NOF divides the level of the attribute nitrate into these four states (these used to be called bands in an earlier version of the NOF): A state: nitrate concentration in the water is <1.0 NO 3 -N/litre B state: nitrate concentration in the water is NO 3 -N/litre C state: nitrate concentration in the water is NO 3 -N/litre D state: nitrate concentration in the water is >6.9 NO 3 -N/litre Each of the other attributes ammonia, dissolved oxygen and periphyton are similarly divided into A, B, C and D states. For a value to be very well provided for, the level of all the associated attributes must fall into the respective A state. On the other hand, should the level of one or more attributes fall into the D state, the associated value will not be achieved. So, what the NOF is saying here is that, in order to ensure good ecosystem health, the nitrate concentration in the water must be less than 1.0 NO 3 -N/litre. This is the A state. On the other hand, the NOF is also warning that, if nitrate concentrations exceed 6.9 NO 3 -N/litre, which is the D state, then ecosystem health will be poor. If a value is regarded as extremely important, then stakeholders will want to make sure it is achieved. In this case, the catchment should be managed to ensure that all the attributes for that value achieve A state within a period of time. On the other hand, if a value is not as important, or a higher state is very difficult to achieve, then it might be sufficient to manage the catchment so that all the attributes for the less-important value achieve B state. This is likely to cost less to achieve, and allow for other uses of the freshwater resource at hand. Returning to our example system, fishing in the North River management unit has been deemed to be very important, so the stakeholders have opted to manage the catchment so that DO achieves the NOF A state and sedimentation rate achieves NOF B state (see extract from Figure 16-3, to the side of this paragraph). The objectives may now be designed to link to the chosen attribute states. For example, an objective might be to achieve the NOF B state sedimentation rate within 10 years over 85% of the North River main stem and to achieve the NOF A state DO within 15 years. Notice that these are Specific, Measurable, Time-bound, and are assumed to be Attainable and Realistic, which makes them SMART. Objectives are what management actually seeks to achieve; attribute states (A, B, C and D in the NOF) are just simple water quality objectives, from which management objectives are formulated. Technical aspects of integrating water quality science in the freshwater and coastal environments 138

149 To review the terminology this far: Value = fishing. Attribute = sedimentation rate. Water quality objective = the NOF B state. Management objective = reduce the annual-average sedimentation rate to the target value within 10 years over 85% of the North River main stem. Other tools that can provide guidance in the process of formulating water quality objectives via an intermediate target include the ANZECC guidelines and local reference data. In some cases, NOF states have actually been formulated from ANZECC guidelines, in which case using the NOF state represents de facto use of the ANZECC guidelines. In other cases, local reference data may need to be developed for use in setting objectives. The NOF is therefore just one of the tools that provides guidance for setting of objectives. The NOF may not always be applicable to the attributes that need to be considered by managers. For instance, in the North River, one of the attributes that needs to be managed to provide for fishing is fish passages. The NOF does not have anything to say about fish passages, so in this case we do not go through the intermediate step of deciding on a desirable attribute state in order to set an objective. However, the guidelines regarding fish passages exist, so here the stakeholders simply refer to those guidelines to develop objectives that relate to fish passages. Figure 16-3 shows examples of using alternative information to the NOF in formulating objectives. STEP 5 Calculating Contaminant Load Limits The NPS-FM requires setting a limit to resource use. Limit is defined quite broadly in the NPS-FM: the maximum amount of resource use available which allows a freshwater objective to be met. Setting a limit to resource use might be just one of the available management options, and a contaminant load limit is just one particular type of limit. For some objectives in our example system, load limits are not relevant. For instance, there is no contaminant load limit that is relevant to the objective associated with the fish-passage attribute in the North River, and there also is no contaminant load limit relevant to the objective associated with the river-edge-habitat attribute in the South River. For some objectives, a limit for only one type of contaminant is needed, but for others limits for more than one contaminant are required. For example, only a metal load limit is required for the heavy-metal objective in the New Estuary 11, but both a sediment load limit and a nutrient load limit are required for the DO objective in the North River. 11 Any heavy-metal attribute will actually be expressed in terms of a sediment concentration, since it is largely through the sediment concentration that effects are exerted. Hence, both a sediment load limit and a heavy-metal load limit would be required to achieve any given heavy-metal attribute state. For simplicity we are disregarding this. Technical aspects of integrating water quality science in the freshwater and coastal environments 139

150 The actual calculation of contaminant load limits might be able to be done simply, by applying guidelines for instance, or it might need to be done with models, which can become complicated. Here is an example of calculating a contaminant load limit by applying guidelines. There are periphyton guidelines that relate periphyton cover to nutrient concentrations in the water. Imagine there is an objective that requires periphyton cover to be no more than 15% of the riverbed by the year 2030 (this objective might have been formulated from a desire to achieve the NOF B state for the periphyton attribute, which in turn needs to be managed to deliver on the value of ecosystem health). One could use the periphyton nutrient relationship to look up the associated nutrient concentrations required to reduce cover to the desired level, and multiply the concentration so obtained by water discharge to come up with a nutrient load limit. Here is an example of calculating a contaminant load limit by using models. Source-to-sea models predict the generation of sediment on the land, transport of the eroded sediment down through the waterway network, and dispersal and deposition of sediment in the coastal marine area. Imagine there is an objective that requires the annual-average sedimentation rate to be 1 mm/year or less, which is designed to return the shellfish harvest to the pre-1950s level (shellfish harvesting is the value being managed for, and the 1 mm/year sedimentation rate is the water quality objective, which is the A state for the attribute sedimentation rate). The source-to-sea model predicts sedimentation rates from input sediment loads; running the model backwards (or inverting the model) will give the sediment load that corresponds to the water quality objective for the sedimentation rate (Green 2013). STEP 6 Reconciling Contaminant Load Limits In this step, we ensure that contaminant load limits add up correctly. Step 6a reconciling contaminant load limits within management units For the clarity objective (designed to deliver the value of swimming in the South River), the sediment load limit was calculated as 1000 units, but for the clarity objective designed to deliver the whitebait value, the sediment load limit was calculated at 2000 units (see extract from Figure 16-3, to the side of this paragraph) 12. Obviously, there cannot be different sediment load limits in the same catchment. Instead, we must pick the smaller of the two as our (single) sediment load limit for the South River catchment; this will allow both objectives to be achieved. Note that in doing this, the whitebait objective will be overachieved (all other things being equal), 12 How can this make sense, when NOF state B is the target for both objectives? Why don t the same NOF states translate into the same sediment load limit? The most likely reason relates to the formulation of the management objectives. For instance, the whitebait objective may allow for the water quality objective to be achieved over a longer timeframe than the swimming objective, which in turn allows for a higher sediment load limit. Technical aspects of integrating water quality science in the freshwater and coastal environments 140

151 which is the price to be paid for simultaneously achieving multiple objectives. In the same way, the conflicting sediment load limits in the North River are reconciled by picking a limit of 600 units (see extract from Figure 16-3, to the side of this paragraph), and the conflicting sediment load limits in the New Estuary are reconciled by picking a limit of 1400 units. No other reconciliations within the management units are required. Step 6b reconciling contaminant load limits across the management units At this point, the sediment load limit for the North River, reconciled within that management unit, is 600 units and the sediment load limit for the South River, again reconciled within that management unit, is 1000 units. But, we have also determined that the sediment load limit for the New Estuary objective (related to a sedimentation rate) is 1400 units (reconciled within the estuary management unit). Now, should the combined North and South River sediment loads deposit in the New Estuary, the estuary sediment load limit will be exceeded. The problem may be solved by reducing the North River limit to 900 units and the South River limit to 500 units, which sum to the estuary s 1400-unit limit (see extract from Figure 16-3, below this paragraph). In this way, the sediment load limits are reconciled across the management units.. We now turn to the microbe limit. We have already determined that the South River microbe limit should be 5000 units, and that the New Estuary limit should be 8000 units. There is no objective for the North River that relates to microbes, but we still need to ensure that the sum of microbes coming from the North and South Rivers does not exceed the estuary load limit. Therefore, we are obliged to set a microbe load limit for the North River of 3000 units (see extract from Figure 16-3, below this paragraph). Note that this Technical aspects of integrating water quality science in the freshwater and coastal environments 141

152 limit for microbes for the North River is required even though there is no objective in that management unit that relates to microbes 13. The process of reconciling contaminant load limits across the management units is equivalent to balancing contaminant budgets. For sediment, the budget was expressed very simply, as: (North River sediment load limit + South River sediment load limit) = New Estuary sediment load limit Other, more sophisticated, budgets could be used, for instance, by accounting for the amount of sediment that is lost from the estuary to the coastal ocean: (North River sediment load limit + South River sediment load limit) = (New Estuary sediment load limit + sediment lost to the coastal ocean) Another version of a budget might account for floodplain deposition between the confluence of the North and South Rivers and the estuary: (North River sediment load limit + South River sediment load limit 13 It is worth noting that in this case other combinations of loads are possible, e.g., South River 2000 and North River 6000 all community/council chosen if economics or existing land use indicate more feasible. Technical aspects of integrating water quality science in the freshwater and coastal environments 142

153 floodplain deposition downstream) = (New Estuary sediment load limit + sediment lost to the coastal ocean) The budget must include all of the management units that are connected by way of contaminant flows. It is best to think about this backwards, starting with the management unit that is at the lowest point in the catchment, as follows. Sediment in the New Estuary arrives from the North River and from the South River. Hence, all of these management units are connected, and so we must reconcile the sediment load limits across all three of these units. It is interesting to note that if we were only considering the North River and the South River, we would see no need to reconcile load limits, because these two units do not exchange sediment. However, when the New Estuary is brought into consideration, the picture changes profoundly. This is the heart of the matter of integrating freshwater and estuarine management : we need to devise management strategies simultaneously that consider both freshwater and estuarine requirements. We now turn to the task of reconciling the nutrient load limits across management units. Nutrients arrive in the estuary from the two rivers, so once more we have to reconcile across all three management units. However, unlike sediments, there is no estuary objective based on a nutrient load limit, so the sum of the two river load limits can be anything, as far as the estuary is concerned. Also, the two rivers do not exchange nutrients, so there is no need to reconcile any nutrient load limit in the North River with any nutrient load limit in the South River. As it turns out, there is no nutrient load limit for the South River, but even if that were not the case, the nutrient load limit of 28 units for North River can be left to stand. Finally, we turn to the heavy-metal load limit. Here, we have set a limit to achieve management objectives only in the estuary. To make sure this is achieved, we have to ensure that management actions, which occur in the catchments of the two rivers, will result in a combined metal load that does not exceed the estuary metal load limit. This requirement is shown in Figure 16-3 under step 7. STEP 7 Management Actions In step 7, we finally decide on what is to be done to achieve the objectives. For those objectives that have related contaminant load limits, we have to ensure our chosen actions will not result in the limits being exceeded. For those objectives that do not have related contaminant load limits, our actions might be related more directly to the objectives. For example, the objective in the North River arising from consideration of the fish passage guidelines might have been construct 28 fish passages beside structures by the year 2022, in which case our management action would be to go out and build 28 fish Technical aspects of integrating water quality science in the freshwater and coastal environments 143

154 passages. We may still need to cast our eyes over the grand scheme here when deciding relatively simple management actions: perhaps the 28 fish passages will somehow affect the amount of sediment reaching the North River, and therefore use up a part of the estuary s 1400-unit sediment load limit The Master Attribute The "master attribute" for sediment is proposed as a measure that would cover cumulative sediment loads, sediment "dumps" and potentially reduction in clarity in the estuarine environment. Other stressors, such as heavy metal concentrations in sediments, might be expected to be correlated with the rate of sediment accumulation but differ depending on predominant catchment land use. Sediment is the basis of the "master attribute" and other associations would need to be established in the development of this parameter. Considering sediment loads alone may not address all values at all estuarine sites and site-specific assessments may also be required. Other master attributes, such as nutrient master attribute or faecal microorganism master attribute may also need to be used for integrated management if values (uses) are affected by those parameters. Using sediment loads as an example we explore the use of this attribute for linking catchment loads with management of estuarine values. It may not always be straightforward or even possible to calculate contaminant load limits required to achieve objectives (in those cases, of course, where an objective does have an associated contaminant load limit). For example, it is possible to calculate a catchment sediment load limit required to achieve a given target annual-average estuarine sedimentation rate 14, but there is no obvious way (yet) to calculate a catchment sediment load limit corresponding to a clarity target or a target related to sediment dumps (Cummings et al. 2003; Norkko et al. 2002; Thrush et al. 2003). However, managing to achieve an annual-average sedimentation rate may reduce the broad spectrum of adverse sediment-related effects, including those related to clarity and sediment dumps. For example it seems unlikely that the measures required in a catchment to reduce annualaverage sediment runoff would not also mitigate the effects of peak storm loads and the discharge of fine sediment to waterways. This raises the issue of managing for a master attribute, which would have the following characteristics: It will be easy to understand and explain. It will be easy enough to measure. It will be correlated with all of the other attributes that could be considered. From this we can infer that changing the state of the master attribute will also change the state of all of the correlated attributes, which in turn will influence the whole suite of related adverse effects. It will be possible to choose the state of the master attribute that is going to achieve any particular objective. 14 By inverting a source-to-sea model, as shown by Green (2013). Technical aspects of integrating water quality science in the freshwater and coastal environments 144

155 It will not be too hard to relate any particular state of the master attribute to a catchment sediment load. In the following we distinguish the master attribute as the sediment master attribute to distinguish it from other master attributes e.g., nutrient master attribute. It is possible that the estuary annual-average sedimentation rate (AASR) could be used as a sediment master attribute. Going through the above list: There are no ambiguities in the meaning of AASR. AASR may be measured in a number of ways (sedimentation plates, repeat bathymetric surveys, for example). Because the annual-average sedimentation rate is the sum of all of the sediment inputs at different frequencies, during different events, and of different types of sediment, then AASR should be correlated with all other sediment-related attributes. If this is the case, then reducing the AASR should also reduce the suite of adverse sediment-related effects that will have a bearing on most objectives. However, this might not be true for every estuary. For example, in the later stages of estuary infilling, when sediment accommodation space (the space available for sediment to deposit) is limited, sediment may not actually deposit to any great extent, but it may still cause adverse effects as it is advected to the sea because of an effect on light climate, for example. In this case, the deposition rate would not be correlated with attributes such as light penetration and visual clarity, and AASR would not be treated as a sediment master attribute if your objective was dependent on light climate. It might be easy enough to choose the desired state of the AASR depending on the management objective. For instance, you might think of the continuum between the pre-catchment-disturbance AASR and the AASR under the present-day catchment land use, both of which are relatively easy to measure, and choose a place where you want to be on the continuum. You would slant your choice to one end or the other depending on your management objectives. It is relatively easy to relate AASR to catchment sediment loads, which provides a basis for limit setting. Figure 16-5 shows how using AASR as a sediment master attribute would fit into the example management scheme, and simplify the limit-setting process. Technical aspects of integrating water quality science in the freshwater and coastal environments 145

156 Figure 16-5 Use of estuary annual-average sedimentation rate (AASR) as a sediment master attribute to simplify limits-based management. Technical aspects of integrating water quality science in the freshwater and coastal environments 146

157 What we are doing here is rolling up the sedimentation rate attribute and the clarity attribute into the master attribute annual-average sedimentation rate. We then decide, by looking at reference data, that <1 mm/year is the water quality objective for AASR. We can then turn that into a management objective (e.g., reduce AASR to an average of 0.9 mm/year in three key shellfish beds by the year 2025) and then calculate the sediment load limit corresponding to that management objective, which is 1200 units. Using the sediment master attribute, we no longer have to calculate a sediment load limit corresponding to any clarity-related objective. But, can we be sure that managing for the sediment master attribute, which is a sedimentation rate, will really deliver the shellfish value, which we know is affected by as far as sediments go both sedimentation rate and clarity? For this, adequate monitoring is required to check that the desired outcomes are in fact being achieved on the back of the sediment master attribute. Auckland Council has started a research project which seeks to investigate the link between coastal sediment accumulation rates to ecological outcomes, to be led by Marcus Cameron (RIMU). The project will test the hypothesis that AASR is correlated with a wide range of indicators of benthic health, which would then open the door to using AASR as a sediment master attribute. The project background sets the scene: SARs are seen as a particularly important policy and planning tool because they provide an integrated measure of chronic and cumulative effects over time, are simpler to predict via modelling than multiple one-off sedimentation events and are the metric that management decisions would expect to influence over long planning horizons. Furthermore, SARs provide an easy concept for the community to understand, current rates can be assessed using sediment plates and historic rates can be assessed from dated sediment cores. For example, SARs are currently being used as a tool to address sedimentation issues caused by land use change in catchments draining to Porirua Harbour. Therefore, establishing a clear link between SARs and benthic ecological effects is seen as critical to their ongoing and robust use in planning decisions and for their successful integration into regional and national policy. The project objective flows accordingly: The primary objective is to develop ecologically relevant and defensible thresholds and limits for SARs to be used in developing and implementing regional and national policy. Technical aspects of integrating water quality science in the freshwater and coastal environments 147

158 Having this information will also help to prioritize catchments at most need of sediment management action by identifying estuarine receiving environments which are close to, or exceed relevant ecological thresholds? The project impact is forecast: Defining the ecological relevance of SARs is critical for their robust use in regional and national policy and to endure scrutiny in council hearings or the Environment Court Conclusions The NPS-FM describes and requires the use of a process for freshwater management that includes setting resource use limits. Where the goods and services provided by freshwater ecosystems are primarily degraded by diffusesource contaminants which is almost always the case in New Zealand limits to resource use will typically, but not always, be in the form of contaminant load limits. There is no requirement to manage estuaries using the NPS-FM process at present. Nonetheless, estuaries must be considered when deciding how to manage freshwater under the NPS-FM. In particular, the process for setting contaminant load limits to achieve freshwater objectives must take into account aspirations for the use of estuaries and vice versa. This requires an understanding of catchment-wide contaminant budgets, and manipulating those budgets to set load limits to simultaneously achieve freshwater and estuary management objectives. Following this process will effectively integrate the management of freshwater and estuaries. There is much practical value in the concept of the master attribute. Research to be pursued by Auckland Council will investigate whether there is a link between sediment deposition rate and benthic ecological effects in estuaries, which could open the door to use of sedimentation as a master attribute that will greatly simplify the establishment of sediment load limits. Technical aspects of integrating water quality science in the freshwater and coastal environments 148

159 17 Potential Conflicts Across All Parameters In this section we identify potential limitations to setting effective and efficient management objectives (narrative), appropriate water quality objectives (numeric), or limits (loads) across both freshwater and coastal environments. The following is applicable to all coastal waters, but we mainly address estuarine receiving waters, because conflicts are more likely to arise than in embayments or open coastal waters. Setting an objectives/limit in a freshwater body will affect the concentrations or loads in a downstream coastal water body (and vice versa). Estuaries are particularly influenced by the quality of the freshwater that flows into them. Potential conflicts arise if the objective/limit set for the freshwater results in the inability to meet objectives/limits set for the downstream coastal receiving water. The simplest case is where numerical objective concentrations are high in freshwater but low in estuaries. An example might be numerical objectives for nitrate concentrations. Limits for controlling nitrate toxicity in freshwater are relatively high concentrations, but management objectives to maintain nitrate concentrations at reference conditions in estuaries, in order to limit water column algal and sediment-associated macroalgal proliferation, will involve very low concentrations of nitrate. Identifying potential conflicts in objective/limit setting is often more complex than merely considering concentrations and dilutions, as described above in our hypothetical example. A water quality parameter may manifest effects in different forms in different water types. As described in the previous section in terms of sediment pollution, clarity a visual measure of TSS during low flows may be the defining issue for freshwater, while total sediment loads largely carried by stormflows are generally more important in terms of impacts on estuaries. However, from the perspective of water resource management, both are related to sediment mobilisation in the contributing catchments, and so ultimately both may need to be controlled by limiting catchment sediment loads. Other freshwater/salt water transitions that may affect a parameter s form and its effects include salt water flocculation of sediments, salt wedges, ionic displacement of metals from SS, change in ph, timing, metal speciation, sediment/nutrient settling, accumulation and in-filling. Technical aspects of integrating water quality science in the freshwater and coastal environments 149

160 For each of the freshwater parameter values examined in this report we identified potential conflicts. 1. There is the simple concentration and consideration of dilution. The nature of the estuary in relation to flushing will be a primary factor affecting dilution of inflows and susceptibility to sediment accumulation. Flushing is a component of the estuarine classification (Hume et al. 2007a) and is a site-specific consideration in relation to the management of each estuary. 2. For each parameter we also considered changes in form and other physico-chemical factors that come into play at freshwater/salt water transitions in the estuary. Table 17-1 identifies potential conflicts that might influence the ability to set effective and efficient narrative and numeric objectives and limits (loads) across both freshwater and coastal environments. Technical aspects of integrating water quality science in the freshwater and coastal environments 150

161 Table 17-1 Potential conflicts and transition issues in setting objectives and limits across both freshwater and coastal environments. Freshwater Estuary Prognosis Temperature N/A No conflict. ph ph The ph in estuaries varies widely from natural freshwater to well buffered marine values of about 8.3. Thus it would be common for ph to vary from about 7 to about 8. Changes in the nature of the freshwater inputs may affect natural ph regime. Potential conflict. Dissolved oxygen (rivers) DO DO concentrations in estuaries should be greater than about 80% saturation. B and C bands in NOF are close to or below 80% saturation. In addition, DO in freshwater discharged to an estuary may be further reduced by sediment and biochemical oxygen demand (SOD and BOD). Temperature and salinity changes may further complicate DO dynamics. (Note there is a general lack of critical information in estuary headwaters). Potential conflict. Clarity (Turbidity) Clarity (Turbidity) Management generally focuses on clarity for rivers during low flow. This will have little influence on coastal waters where clarity is more often related to wave resuspension and flood flows. Turbidity maxima in estuaries occur in the freshwater/estuarine transition zone are driven by estuarine particle recycling processes so are not directly related to freshwater turbidity. Internal recycling driven by wind/wave resuspension within the estuary may result in a sustained degraded condition. However, management of an estuary for macrophytes (e.g., eel grass, Zostera) will require consideration of light (i.e., turbidity and depth) and sediment characteristics (e.g., muddiness, nutrients, ammonia). Thus an integrated assessment of multiple factors will be required for macrophyte management. Potential conflict. Salinity (conductivity) Salinity No conflict. Technical aspects of integrating water quality science in the freshwater and coastal environments 151

162 Freshwater Estuary Prognosis Sediment/Suspended Solids Total Nitrogen (lakes) - usually loads Total Phosphorus (lakes) Nitrate toxicity (lakes and rivers) Sediment Deposition Rate (SDR) Muddiness TN load to estuary, TN concentration in sediments (TN load can be related to TN concentration (and potentially pore water ammonia) in sediments. TP load, TP concentration in sediments. (TP load can be related to TP concentration in sediments} Nitrate toxicity Catchment mass load limits in rivers could control SDR or muddiness in coastal areas. A suspended solids (and turbidity) maxima in estuaries occur in the freshwater/estuarine transition zone are driven by estuarine particle recycling processes so are not directly related to freshwater turbidity. Internal recycling driven by wind/wave re-suspension within the estuary may result in a sustained degraded condition. Need for integrated approach (loads, TSS) as described in Section 3.6 above. Potential conflict. Lakes and estuaries are not connected, so there is no direct conflict. TSS and TN are correlated in catchment loads and concentrations. Therefore, there is a potential conflict between specifying TSS and TN loads to estuaries, and hence the potential for conflict between TSS limits in freshwater and TN limits in estuaries. Potential conflict. Lakes and estuaries are not connected so there is no direct conflict. TSS and TP are correlated in catchment loads and concentrations. However, there is no direct conflict between fresh and marine because eutrophication in estuaries is not usually phosphorus limited and not managed by setting limits on TP. No conflict. Nitrate guidelines for marine waters are markedly higher than all freshwater guidelines. No conflict. Technical aspects of integrating water quality science in the freshwater and coastal environments 152

163 Freshwater Estuary Prognosis Ammonia Toxicity (Ammoniacal Nitrogen) (lakes and rivers) Ammonia Toxicity Ammonia limits may be more stringent in marine than fresh waters, because of higher seawater ph, counteracted to some degree by higher salinity. So may need to need consider dilution/ph/salinity effects in special cases involving larger ammonia mass loads; these circumstances are expected infrequently, if at all. Sediment pore water concentrations of ammonia will increase with high TN loads. High pore water ammonia concentrations may adversely affect infaunal species and the survival of desirable macrophyte species (e.g., eel grass, Zostera). The current revision of the ANZECC guidelines includes a revision of the ammoniacal nitrogen guidelines with ph and temperature dependence. Potential conflict. Dissolved nutrients (nitrogen and phosphorus) Chlorophyll a (in lakes) It is possible that dissolved nutrients will be specified in relation to reference conditions as a simple assessment for eutrophication (this currently occurs in an ad hoc fashion in NZ using ANZECC physico-chemical guidelines) Chlorophyll a Conflicts are likely for dissolved nutrients, if dissolved nutrients are specified for rivers (e.g., nitrate toxicity) and for estuaries (e.g., reference conditions). This could be easily checked by comparing concentrations after taking dilution into account; dilution may be estimated using salinity. The primary nutrient of concern is inorganic nitrogen which is expected to be the limiting nutrient in most marine environments. A lack of marine guidelines for eutrophication nitrogen currently limits assessment of potential effects. Potential conflict. Chlorophyll is not usually specified for rivers but is for lakes, but these are not connected to estuaries. No conflict. Technical aspects of integrating water quality science in the freshwater and coastal environments 153

164 Freshwater Estuary Prognosis Macrophytes (currently no guidelines) Macrophytes (currently tentative guidelines) Generally there are no obvious conflicts in specifying macrophytes growth and extent in either media. Growth of macroalgae in estuaries and macrophytes in freshwater may be driven by similar processes (nutrients and light are major factors). To date, tentative limits have been set for nutrient loads or sediment concentrations in marine waters. For freshwater, dissolved nutrients have been used to limit periphyton, but there are no nutrient guidelines for macrophytes. Some estuarine macroalgae are considered nuisance growths (e.g., Ulva) while others are highly desirable ecosystem components and the focus of management and restoration programmes (e.g., eel grass, Zostera). No immediate conflict exists, but reassessment will be required if nutrient guidelines are used to manage macrophytes in the future. Management objectives for estuaries will require site-specific considerations. Potential conflict. Periphyton (rivers) N/A No conflict. Microbiological e.g., E. coli, cyanobacteria (planktonic) (lakes and rivers) Enterococci, E. coli (in special cases) If lower target bands are specified for a freshwater flow which discharges near a coastal beach, then potential conflicts will need to be assessed. This is somewhat complicated in the general case when specifying different indicators for different media. Such conflicts may be better first addressed using the MfE (2003) catchment sanitary assessments when calculating beach grades. Primary contact recreation is a major activity in estuaries and coastal lagoons. Therefore, estuarine objectives are expected to be controlling factors for freshwater loads of faecal microorganisms. Potential conflict. Technical aspects of integrating water quality science in the freshwater and coastal environments 154

165 Freshwater Estuary Prognosis Heavy metals (e.g., copper, zinc, lead, cadmium) in water and in sediments. Macroinvertebrate (MCI) Heavy metals (e.g., copper, zinc, lead, cadmium) in water and in sediments. Various measures of macroinvertebrate health In water, criteria commonly used (based on ANZECC 2000) are similar in fresh and marine water, so there are no conflicts. However, changes in speciation and toxicity with changes in salinity, ph and accompanying desorption/adsorption processes occurring in the freshwater/estuarine transition zone are not being taken into account currently. If future criteria include speciation assessments as described earlier, or the development of different levels of protection (and hence attribute bands), or involve loads of heavy metals then conflicts will need to be reassessed. Heavy metals and TSS are correlated in catchment loads and concentrations. Therefore, there is a potential conflict between specifying TSS and heavy metal loads to estuaries, and hence the potential for conflict between TSS limits in freshwater and heavy metal limits in estuaries. Potential conflict. Macroinvertebrate health measures are not related across media. No conflict. Fish productivity (IBI) Quota data Many New Zealand freshwater fish are diadromous and, estuarine water/freshwater transition issues are possible when fish migrate. Potential conflict. Stream Ecological Valuation (SEV) N/A Not related. No conflict. Lake SPI N/A Not related. No conflict. Lake Trophic Index (LTI) Fish productivity (QIBI) N/A N/A Not related. No conflict. Many New Zealand freshwater fish are diadromous and, estuarine water/freshwater transition issues are possible when fish migrate. Potential conflict. Technical aspects of integrating water quality science in the freshwater and coastal environments 155

166 Freshwater Estuary Prognosis CCME Water Quality Index, ARC index N/A Conflicts unknown and not expected. The indicators break down into three categories as shown in Table 17-2: 1. No conflict. 2. Transition issues depending on physico-chemical factors in the freshwater/estuarine transition zone. 3. Potential conflict. Most parameters fall into the first category. A few fall into the second transition category because the potential for conflict exists depending on physico-chemical factors or multiple factors needing consideration for ecological effects. Those that fall into the third Potential conflict category relate either to: particulate matter transported through riverine systems to estuaries, where they can accumulate (i.e., mass load issues identified by M in Table 17-2), or dilution considerations, where levels of dissolved parameters in rivers may be too high to protect migrating fish species or estuaries after discharge and dilution. The parameters with transition issues arise from the physico-chemical changes occurring in transitioning from the freshwater to the estuarine environment. One of these transition changes results in turbidity maxima, with associated changes in the settling of suspended solids and in the release of metals bound onto the suspended solids. These marked chemical changes will often result in conditions in the estuarine environment that are not readily predicted from simple consideration of the freshwater parameter concentrations (e.g., clarity, TSS concentrations, dissolved /total metal concentrations). Thus concentration and fate predictions for these parameters will often have a low reliability and require specific investigations. Complex relationships also exist between TSS, nutrients (TN and TP) and heavy metals, because suspended sediment carries associated nutrients (particulate nitrogen and phosphorus) and particulate metals. If estuarine guidelines are set Technical aspects of integrating water quality science in the freshwater and coastal environments 156

167 for more than one of TSS, TN, TP or heavy metals, the guideline with the lowest TSS load will set the limiting management load. The potential for conflict can be assessed by comparing any specified nutrient or metal load with the load of particulate nutrient or metal associated with a specified sediment load. This assessment requires knowledge of the total concentration of nutrient and/or metals in freshwaters. Providing general guidance recommendations on how to address and resolve areas of potential conflict in setting objectives between freshwater and estuarine environments is difficult. Downstream sensitivity will in some circumstances dictate the upstream management requirements (and vice versa). This difficulty in providing guidance arises because of a number of factors, including: (i) the complex nature of the transitions outlined above; (ii) lack of guidelines for ecosystem effects in the estuarine environment (e.g., for nutrients and sediments); (iii) site-specific nature of estuaries (e.g., freshwater inflows, flushing); (iii) biotic sensitivity of estuary receiving environment; and (iv) undefined or differing values between estuaries. Currently a framework for the integrated management is not available. In the short term, conflicts would be best addressed on a case-by-case basis. In due course, a systematic approach may be developed to establish freshwater and estuarine values and to reconcile the conflicts that are identified. Such a process will require standard guidance and the incorporation of pragmatic approaches to resolve the challenges posed by often limited data availability, and the need for timely decision-making. Technical aspects of integrating water quality science in the freshwater and coastal environments 157

168 Table Potential conflicts and transition issues in setting attribute limits in freshwater and coastal waters. Parameter setting Freshwater Limit Temperature Issues a No conflicts X Transition b Potential conflicts ph W X Dissolved oxygen W X Clarity (turbidity) W, M, I, T X X Salinity (conductivity) Sediment/Suspended Solids X W, M, I, T X X Total Nitrogen c W, M, I X X Total Phosphorus Dissolved nutrients W X Chlorophyll a Periphyton (rivers) NA X Ammonia Toxicity W, T, (M) X X Nitrate toxicity Heavy metals c W, M, I, T X X X Microbiological W, M, I X Stream Ecological Valuation (SEV) NA Macroinvertebrate (MCI) NA X Macrophytes d d X Lake SPI NA X Fish productivity (IBI) W, M, T X Fish productivity (QIBI) W, M, T X Lake Tropic Index (LTI) NA X CCME Water Quality Index, ARC index X X X X X a Issues for potential marine environment effects for this parameter: W = water column only; M = mass load (settling and cumulative effects); I = internal recycle within estuary; T = transition effects (see below); NA = parameter not applicable to marine environment. Bracketed indicates parameter which may be sensitive to high freshwater mass loads. b The Transition category identifies parameters which exhibit marked changes in physical properties or toxicity (e.g., ph and salinity affect ammonia toxicity) in transitioning from fresh to marine water. c Potential conflicts scored for multiple categories because of the potential for site-specific effects. See text for discussion. d Macrophyte proliferation or die-off are often major estuarine management issues, however, freshwater state is not an indicator of an estuarine value. Technical aspects of integrating water quality science in the freshwater and coastal environments 158

169 18 Summary Auckland Council is currently engaged in a number of significant programmes and projects that focus on how Auckland s natural resources are managed. Two of these programmes are in response to changes at a national level, the National Policy Statement: Freshwater Management 2014 (NPS-FM) with implementation through council s Freshwater Programme Wai Ora Healthy Waterways and Marine Spatial Planning (MSP) as a preliminary means of addressing aspects of the New Zealand Coastal Policy Statement (NZCPS). There is a clear overlap between the two programmes in the area of water quality, not least the natural river to sea connection between the land, fresh water and coastal environments. A key area of overlap occurs around water quality parameters and the setting of objectives and limits. The latter are required in fresh water by the NPS-FM, whereas objectives and limits are not required by the NZCPS in the coastal environment (though the intent is indicated in Policy 7). It is envisioned that determining values, and developing objectives and limits for the coastal environment would be the logical next steps arising from the MSP process. As a first step, in 2012 Auckland Council commissioned a report which provided a preliminary assessment of limits and guidelines available for classifying coastal waters (Williamson et al. 2016). A similar investigation focusing on the freshwater environment was identified as necessary to develop NPS-FM implementation strategies. The information from the two studies could then be used to guide application of scientific knowledge of water quality to an objectives and limits framework, thereby supporting uses and values of Auckland s fresh and coastal water resources in an integrated manner. The purpose of this report is to provide: a technical assessment of the existing guidelines and limits used to classify fresh water for water quality management purposes, and an understanding of the technical considerations required to integrate coastal and freshwater science for the purposes of establishing objectives and limits under the National Policy Statement: Freshwater Management 2014 and the New Zealand Coastal Policy Statement. In this report, we summarise chemical, biological and physical guidelines that would be useful in managing Auckland s fresh waters. Technical aspects of integrating water quality science in the freshwater and coastal environments 159

170 For waters used for drinking water, contact recreation, irrigation and stock watering purposes, standards and guidelines are well established. Application and use of these standards and guidelines is relatively straightforward because management relates principally to achieving specific numeric values for water quality parameters. We recommend that the primary documents (e.g., ANZECC, Ministry of Health) are used for these values (uses). For other uses (for example, ecosystem health), guidelines are less clear. Management requires an integrated assessment approach, including a wide range of water quality, habitat, biological and geomorphological parameters. We recommend the use of the National Objectives Framework (NOF) standards; where specific water quality parameters are missing from the NOF, the ANZECC guidelines approach may be followed to fill these gaps. However, unlike NOF standards which are numeric objectives, ANZECC guidelines are trigger guidelines thresholds, exceedances of which trigger further work and include two types of trigger values (physico-chemical guidelines derived from reference sites and toxicant guidelines relating to chronic effects on species). Consequently, we point out that uncritical use of the physico-chemical numerical trigger values listed in the ANZECC guidelines actually contradicts the ANZECC guidelines approach. Some numerical guidelines are not appropriate to Auckland, and, consistent with the ANZECC guideline approach, local numerical objectives have to be derived for some parameters using data collected from suitable reference sites. The ANZECC guidelines are undergoing revision we have indicated likely changes and tried to factor these into the review as far as possible. Narrative objectives will need to be used in regional plans to cover habitat-related issues, and a range of quantitative approaches may be used where habitat management is required to protect freshwater values (uses). Other biological and physical guidelines relevant for managing Auckland s fresh waters are not found in the NOF or ANZECC guidelines. Many of these have been developed in New Zealand (including Auckland). Some of these may be used directly, while others require development and ratification for use in Auckland (e.g., SEV, Fish IBI, macrophyte indices, MCI and variants). Table 18-1 summarises our evaluation of guidelines for environmental parameters for freshwater. A succinct summary of the physical, chemical, biological guidelines that will assist management of Auckland s freshwater is given in Table 18-2, where attributes are associated with values. The table provides a status of the guidelines for various attributes, indicates where guideline development is Technical aspects of integrating water quality science in the freshwater and coastal environments 160

171 required, indicates where a limits approach could be used, and ranks the attribute in terms of importance in defining Auckland s freshwater values. The table lists: Values = which values are applicable for this attribute. Guidelines available = whether general guidelines are available for that attribute. Based on = the type of guideline and/or its derivation. Guidelines needed for freshwater bodies in Auckland = which freshwater receiving waters would require guidelines - All, soft-bottomed streams, hard-bottomed streams, lakes, groundwater. Guideline development needs or strategies = where guidelines will need to be developed for Auckland conditions. Numerical objectives = whether numerical objectives can be derived for Auckland. Limits approach possible = where numerical objectives could be translated into a catchment and discharge limits approach. Importance = the relative importance of the attribute in managing Auckland s freshwaters. The potential for management conflicts in setting limits in freshwater and downstream coastal water was explored. Table 18-3 identifies potential conflicts/transition issues that might influence the ability of resource managers to set effective and efficient objectives and limits across both fresh water and coastal environments. Table 18-1 Recommendations for Guidelines for Environmental Parameters. Parameter Temperature Recommendations The proposed NOF bands for Maritime Regions are recommended for management of Auckland s streams, rivers, lakes (and groundwaters) and are a substantial improvement from the standards promulgated under the RMA. Changes include different levels of protection, recommendations for actual temperature upper limits (rather than changes), the need for continuous monitoring, and the need to consider DO and ph when considering temperature. Alternative tables are also available for site-specific application to a local reference condition approach. Technical aspects of integrating water quality science in the freshwater and coastal environments 161

172 Oxygen Salinity ph Parameter Clarity and colour Total suspended solids (TSS) Ammonia Nitrate Metals and metalloids in water Recommendations The numerical standard of 80% saturation in the RMA to protect aquatic organisms is to be succeeded by more rigorous NOF bands, which are recommended for use in Auckland s freshwater streams and rivers. The bands specify DO concentrations over 1 and 7-day periods and require continuous monitoring. Consequently, the monitoring requirements for DO, if it is a desirable attribute for ecosystem health and other values involving healthy aquatic organisms, will become more rigorous than in the past. Guidelines are available for salinity for drinking water, and for salt tolerance for irrigation of plants. Where salinity changes are of concern for aquatic organisms, ANZECC guidelines recommend a reference condition approach, where the allowed changes are specified as proportional changes from reference conditions (e.g., 20%). We recommend the proposed NOF bands which are similar or slightly more rigorous than guidelines used in the past. However, management of this attribute for ecosystem health (and other related values such as fisheries, fish spawning, aquaculture, mahinga kai, natural waters) will require more rigorous monitoring (continuous over summer) than was typically undertaken in the past (spot measurements at infrequent time intervals e.g., monthly), which places a greater burden on monitoring programmes. Guidelines for clarity and optical characteristics have been in use for several decades, are reasonably robust and are widely accepted. This partly stems from the early guidance in the 1991 RMA that there will be no change in colour or visual clarity following the discharge of contaminants. It is likely that this will be a key attribute for the values contact recreation and aquatic ecosystems in the Auckland region, as well as other values that involve the continued viability of aquatic organisms. Because clarity is a major factor in the public perception of water quality it will be also important in natural form and character and mahinga kai. Reference sites should be used to establish clarity range in natural environments. River clarity may be an important parameter when estuarine macrophytes are a management issue. Given the importance of sediment impacts in the Auckland region, the relative rarity of hard-bottomed streams, and the near-pristine environments that many of these streams occur in (Hunua Ranges, Waitakere Ranges, Great Barrier Island) these guidelines should be a primary management tool (in NOF language a key attribute) for these aquatic hard-bottomed environments. Guidelines for depositional sediment in rivers are currently being developed as part of the NOF. Limits may be required for rivers or effects on downstream estuarine environments, or for related parameters such as clarity and turbidity affecting aesthetics and plant growth (see Clarity and colour). We recommend that the NOF Numeric Attribute State for different levels of protection are used, which will require measurement of temperature and ph. We recommend that the NOF Numeric Attribute State for different levels of protection are used. We recommend that guidelines for different levels of protection for dissolved (i.e., filterable) Cu and Zn are adopted from the revised ANZECC guidelines. The current ANZECC (2000) guideline trigger values are under review and there is likely to be a small change in values. Technical aspects of integrating water quality science in the freshwater and coastal environments 162

173 Parameter Organics in water Nutrients Human Health Stream Ecological Valuation (SEV) Recommendations We recommend that guideline for different levels of protection for total organics are adopted from the revised ANZECC guidelines. Nutrient enrichment resulting in periphyton blooms is not a major issue in Auckland rivers. In Auckland s hard-bottomed streams, focus should be more on maintaining or providing riparian cover and shade. Periphyton respond mainly to dissolved nutrients. Macrophytes in unshaded, soft-bottomed lowland streams can be a major feature and affect water quality (e.g., dissolved oxygen). Recommendations for their measurement and provisional guidelines are described. Maintaining and providing riparian cover and shade should also be management priority. Macrophytes respond mainly to total nutrients, which may settle and accumulate as particulate matter within macrophyte beds. Excessive accumulation of organically enriched sediments may also result in toxic levels of sediment ammonia, which may adversely affect sensitive macrophyte species. Nutrient enrichment is a major issue for many Auckland lakes. NOF standards for total nitrogen, total phosphorus and chlorophyll a are applicable to provide guidance to prioritise management, along with the application of LakeSPI for native and exotic macrophyte monitoring. Catchment load limits may need to be established using suitably calibrated models (e.g., CLUES) for lakes which do not meet acceptable standards for use. Downstream estuarine environments may be affected by dissolved and particulate nutrients primarily nitrogen resulting in water and sedimentassociated algal blooms. Excessive accumulation of organically enriched sediments may also result in toxic levels of sediment ammonia, which may adversely affect sensitive macrophyte species. The NOF bands for secondary contact are mandatory, while the bands for primary contact are optional. The current MfE criteria are appropriate for Auckland bathing situation. Catchment modelling, which is in its infancy, should be continued to be developed, to see if this will yield a robust catchment-specific limit-based approach to managing microbiological pollution. Problem sites are generally downstream of catchments with significant development (urban, pastoral) and wastewater overflow problems. Monitoring should be carried out near wastewater outfalls, to ensure treatment is sufficient and risks to contact recreation in these areas are very small. Quantitative microbial risk assessment (QMRA) should be continued to be used to assess health risks associated with sewage discharges. The genotyping approaches look to be very promising and Auckland Council should keep a watching brief on developments overseas. SEV is highly relevant as an integrated measure of stream ecological integrity, incorporating biological and physical attributes and (inferred) chemical processes. At present there are no published guidelines for assessing SEV scores, e.g., as poor, fair, good or excellent. There are unpublished guidelines used in Auckland Council SoE report cards that could be developed as guidelines based on reference conditions. Technical aspects of integrating water quality science in the freshwater and coastal environments 163

174 Parameter Macroinvertebrate Community Index (MCI) Bacterial Community Index (BCI) Stream macrophytes LakeSPI Recommendations MCI is recommended alongside measures of water quality and habitat quality for summarising the ecological health of Auckland streams. The soft-bottomed version of MCI (sb-mci) should be used in place of the hb-mci for naturally softbottomed streams, which comprise the majority of Auckland streams. In some cases, MCI could be used in combination with QMCI or SQMCI, as the latter are able to detect small and medium changes in stream health. In addition, other biotic indices such as Total taxa richness, EPT taxa richness and %EPT abundance should also be used as these show different aspects of the macroinvertebrate community (i.e., structure and composition in addition to tolerance), and they may be sensitive to impacts that MCI is not. A combined index such as Average Score Per Metric or the Invertebrate Fauna Intact function from SEV may perform better than MCI or any other single index in discriminating sites at all levels of human impact. Further development of the BCI is not recommended. We recommend using the percentage of stream cross-sectional area or volume and the percentage of stream surface area occupied by macrophytes of different species for assessing macrophytes as both indicators and agents of stream degradation for ecosystem health and flow conveyance, and for human recreation and aesthetics. The provisional guidelines of Matheson et al. (2012) could be adopted in the interim, and refined if necessary by Auckland Council with application and accumulated experience. Because macrophytes have both positive and negative characteristics, further studies are needed for guideline development and to determine optimum control strategies. LakeSPI is recommended as a simple, cost-effective method for monitoring the ecological condition of lakes. Because LakeSPI responds to somewhat different environmental conditions than other lake indices such as the Lake TLI, and focuses on the littoral zone rather than the open water environment, it should complement, rather than replace, physico-chemical monitoring of lakes. LakeSPI is recommended every 1-3 years for lakes where change is expected, or risk of invasion is high, but can be relaxed to 10 years or so for lakes that are considered stable. Technical aspects of integrating water quality science in the freshwater and coastal environments 164

175 Parameter Fish Index of Biological Integrity (IBI) Lake Trophic Level Index (TLI) Water Quality Index (WQI) Other Recommendations The Fish IBI is recommended as the best available index for assessing the ecological integrity of the fish community. The quantile version of the Fish IBI (Fish QIBI) is believed to be more accurate than the non-quantile version, but care must be taken not to mix results between the two methods, as the Fish QIBI produces higher values than the Fish IBI. Many factors impacting on fish communities occur at catchment rather than local site scales. Therefore, instead of reporting Fish IBI scores by individual site, it may be more appropriate to combine them from all sites in a catchment into a single catchment-scale score. The known altitude-related migratory abilities for some native fish species needs to be considered in the design of the monitoring programme. Alternatively, it may be better to use an index that uses catchment scale data directly (e.g., SIFR, described below). Sampling should only take place in late summer, as this is when maximum species diversity occurs in New Zealand streams because all diadromous species are present in fresh water. The full range of habitat types present at a site should be sampled. The TLI is recommended as suitable for assessing the trophic state of freshwater lakes in Auckland. It is particularly robust for monitoring changes in trophic state in individual lakes over time. We adopt the recommendation in NEMaR of monthly determination of TLI, because many Auckland lakes are shallow and hence subject to rapid change, and because trend analysis requires a high frequency of sampling. The Auckland Council WQI is based on the Canadian WQI method and is currently used for SoE reporting. It is based on seven water quality parameters (dissolved oxygen, ph, turbidity, ammoniacal nitrogen, temperature, total phosphorus, total nitrogen), with physico-chemical objectives derived from the 98 th percentile value of the parameter using data from three regional reference sites. This approach is similar to the physico-chemical trigger values in the ANZECC (2000) guidelines, which use an 80 th percentile of the reference site water quality as the guideline value. Both the ANZECC physico-chemical trigger values and the Auckland Council WQI are based on a reference site approach, and therefore, do not provide a measure of adverse biological effects in the rivers. We recommend that the Auckland Council maintains a watching brief on future development of methods similar to the CCME WQI. Future developments of the Auckland Council WQI could be based on either the reference site approach or the NOF standards for either approach, consistent application of the methods and interpretation of the results are essential, and details describing the underlying principles and working of the indices should also be reported. A range of habitat-related issues also need to be addressed to provide suitable ecological habitats in rivers, streams and lakes. These include: flows (minimum and peak), riparian shade, refugia (e.g., stones and logs), migration barriers for fish and invasive species. Management for ecosystem health cannot be successfully undertaken without holistically addressing both water quality and the habitat-related factors. Notes: Tables are provided for thermal stress bands for Eastern Dry climate, Maritime climate and for application on a site-specific basis to local reference site data. Technical aspects of integrating water quality science in the freshwater and coastal environments 165

176 Table 18-2 Summary of guidelines status for Auckland s freshwaters. SB = soft-bottom; HB = hard-bottom. Attribute Values in Auckland region Guidelines available? Based on Guidelines needed for FW bodies in Auckland? Development need or strategy Numerical objectives Limits approach possible? Importance Temperature Dissolved oxygen (DO) Salinity Ecosystem health 15, fish spawning, mahinga kai, natural state Ecosystem health 1, fish spawning, mahinga kai, natural state Drinking water, irrigation Yes NIWA draft NOF guidelines Yes, especially lowland SB streams Could link to shade guidelines Yes, proposed bands available Yes NOF All - Yes, bands available Yes Yes for wastewater discharges, challenging otherwise Yes ANZECC No - Yes No Low Moderate High 15 Includes aquaculture should this ever be developed in Auckland freshwaters (e.g., koura) Technical aspects of integrating water quality science in the freshwater and coastal environments 166

177 Attribute Values in Auckland region Guidelines available? Based on Guidelines needed for FW bodies in Auckland? Development need or strategy Numerical objectives Limits approach possible? Importance ph Clarity Ecosystem health Ecosystem health (?) 16, primary and secondary contact, aesthetic-visual amenity, natural state, mahinga kai Yes NIWA draft NOF guidelines Turbidity See clarity None All surface (surrogate for clarity) Fine sediment cover, sediment size, suspendable sediments Periphyton Ecosystem health, natural state, aestheticvisual amenity Ecosystem health, aesthetic/visual amenity SB streams - Yes Yes Moderate Yes MfE guideline All surface - Yes Challenging High Interim proposed for HB streams Interim guidelines and reference conditions for HB streams HB streams Develop clarity/turbidity relationships Ratify for Auckland HB streams. Guidelines for SB streams Yes Yes Challenging Clarity preferred Challenging High Yes NOF HB streams Yes Challenging Low/Moderate 16? indicates adverse effects not expected from this attribute but could occur in extreme circumstances Technical aspects of integrating water quality science in the freshwater and coastal environments 167

178 Attribute Values in Auckland region Guidelines available? Based on Guidelines needed for FW bodies in Auckland? Development need or strategy Numerical objectives Limits approach possible? Importance Dissolved N&P Ecosystem health, aesthetics, natural state Yes MfE Guidelines for HB streams + Reference conditions HB streams Reference conditions Yes Challenging Low Total N&P Ecosystem health, aesthetics, natural state Yes NOF + Reference conditions Yes (lakes) Reference conditions Yes Yes High N&P in stream sediments Ecosystem health No Reference conditions SB lowland streams Reference conditions No Yes Low Zn, Cu in water Ecosystem health Yes ANZECC HB streams, SB streams Reference conditions + best management practice Yes Challenging for dissolved High Ammonia Ecosystem health Yes NOF HB streams, SB streams Yes Yes Low Nitrate Ecosystem health, drinking water E. coli Primary and secondary contact, mahinga kai, stock water Faecal coliforms Shellfish, mahinga kai Yes Yes NOF (streams), MOH (groundwater) NOF, MfE/MOH Streams, drinking water supplies Yes MfE/MOH Streams and lakes Yes Yes High (GW) Moderate (streams) All Yes Challenging High Yes Challenging Moderate/High Technical aspects of integrating water quality science in the freshwater and coastal environments 168

179 Attribute Values in Auckland region Guidelines available? Based on Guidelines needed for FW bodies in Auckland? Development need or strategy Numerical objectives Limits approach possible? Importance Quantitative Microbial Risk Assessment (QMRA) Shellfish, mahinga kai, primary and secondary contact Genotype, viruses Primary and secondary contact, mahinga kai Cyanobacteria Stream Ecological Valuation (SEV) Macroinvertebrate Community Index (MCI) Bacterial Community Index (BCI) Ecosystem health(?) 2, primary and secondary contact, natural state, mahinga kai Ecosystem health, natural state, mahinga kai Ecosystem health, mahinga kai Ecosystem health Yes Norovirus survival and rates of infection All Norovirus infection and survival info Yes Yes for point sources High for any WWTP discharge No Under international development Watch Yes NOF Lakes Streams Yes No Moderate (lakes) Yes Proposed (NOF) No Reference conditions National reference conditions Reference conditions HB streams, SB streams HB streams, SB streams HB streams, SB streams Reference conditions and ecological gradients Reference conditions and ecological gradients Yes No High Yes No High No Low Technical aspects of integrating water quality science in the freshwater and coastal environments 169

180 Attribute Values in Auckland region Guidelines available? Based on Guidelines needed for FW bodies in Auckland? Development need or strategy Numerical objectives Limits approach possible? Importance Stream macrophytes Ecosystem health, aesthetics Yes Reference conditions HB streams, SB streams Link to riparian planting, minimum flows Yes No Moderate/High LakeSPI Ecosystem health, aesthetics, natural state, mahinga kai No Reference conditions Lakes Base guidelines lake restoration strategies Possible No Moderate Lake Trophic Level Index (TLI) Ecosystem health, aesthetics, natural state, mahinga kai Yes Trophic responses Lakes Harmful algal blooms (see cyanobacteria) /trophic status links Yes Yes Moderate Fish IBI Ecosystem health, natural state, mahinga kai No Reference conditions All Develop regional guidelines. Relate to habitat and passage. Yes No High Water Quality Index (WQI) Ecosystem health, natural state, mahinga kai Yes Composite of multiple guidelines or reference site benchmarks related to values (uses) All Currently used by Auckland Council for SoE reporting for streams (relative to reference site benchmarks, i.e., natural state conditions). Investigation needed. Possible No Low/Moderate Technical aspects of integrating water quality science in the freshwater and coastal environments 170

181 Table 18-3 Potential conflicts and transition issues in setting attribute limits in fresh water and coastal waters. Parameter setting Freshwater Limit Temperature Issues a No conflicts X Transition b Potential conflicts ph W X Dissolved oxygen W X Clarity (turbidity) W, M, I, T X X Salinity (conductivity) Sediment/Suspended Solids X W, M, I, T X X Total Nitrogen c W, M, I X X Total Phosphorus Dissolved nutrients W X Chlorophyll a Periphyton (rivers) NA X Ammonia Toxicity W, T, (M) X X Nitrate toxicity Heavy metals c W, M, I, T X X X Microbiological W, M, I X Stream Ecological Valuation (SEV) NA Macroinvertebrate (MCI) NA X Macrophytes d d X Lake SPI NA X Fish productivity (IBI) W, M, T X Fish productivity (QIBI) W, M, T X Lake Tropic Index (LTI) NA X X X X X CCME Water Quality X Index, ARC index a Issues for potential marine environment effects for this parameter: W = water column only; M = mass load (settling and cumulative effects); I = internal recycle within estuary; T = transition effects (see below); NA = parameter not applicable to marine environment. Bracketed indicates parameter which may be sensitive to high freshwater mass loads. b The Transition category identifies parameters which exhibit marked changes in physical properties or toxicity (e.g., ph and salinity affect ammonia toxicity) in transitioning from fresh to marine water. c Potential conflicts scored for multiple categories because of the potential for site-specific effects. See text for discussion. d Macrophyte proliferation or die-off are often major estuarine management issues, however, freshwater state is not an indicator of an estuarine value. Technical aspects of integrating water quality science in the freshwater and coastal environments 171

182 The indicators break down into three categories as shown in Table 18-3: 1. No conflict. 2. Transition issues depending on physico-chemical factors in the freshwater/estuarine transition zone. 3. Potential conflict. Most parameters fall into the first category. A few fall into the second transition category because the potential for conflict exists depending on physico-chemical factors or multiple factors needing consideration for ecological effects. Those that fall into the third Potential conflict category relate either to: particulate matter transported through riverine systems to estuaries, where they can accumulate (i.e., mass load issues identified by M in Table 18-3), or dilution considerations, where levels of dissolved parameters in rivers may be too high to protect migrating fish species or estuaries after discharge and dilution. The parameters with transition issues arise from the physico-chemical changes occurring in transitioning from the freshwater to the estuarine environment. One of these transition changes results in turbidity maxima, with associated changes in the settling of suspended solids and in the release of metals bound onto the suspended solids. These marked chemical changes will often result in conditions in the estuarine environment that are not readily predicted from simple consideration of the freshwater parameter concentrations (e.g., clarity, TSS concentrations, dissolved/ total metal concentrations). Providing general guidance recommendations on how to address and resolve areas of potential conflict in setting objectives between freshwater and estuarine environments is difficult. Downstream sensitivity will in some circumstances dictate the upstream management requirements (and vice versa). This difficulty in providing guidance arises because of a number of factors, including: (i) the complex nature of the transitions outlined above; (ii) lack of guidelines for ecosystem effects in the estuarine environment (e.g., for nutrients and sediments); (iii) site-specific nature of estuaries (e.g., freshwater inflows, flushing); (iii) biotic sensitivity of estuary receiving environment; and (iv) undefined or differing values between estuaries. Currently a framework for the integrated management is not available. In the short term, conflicts would be best addressed on a case-by-case basis. In due course, a systematic approach may be developed to establish freshwater and estuarine values and to reconcile the conflicts that are identified. Such a process will require standard guidance and the incorporation of pragmatic approaches to resolve the challenges posed by often limited data availability, and the need for timely decision-making. Technical aspects of integrating water quality science in the freshwater and coastal environments 172

183 19 Abbreviations and Glossary 19.1 Abbreviations Acronym Definition: (relevant environment) AASR Average Annual Sedimentation Rate (estuaries) ACR Acute to Chronic Ratio ANZECC Australian and New Zealand Environment and Conservation Council ASPM Average Score per Metric BOD Biochemical oxygen demand BLM Biotic Ligand Model CAV Cross-sectional area or volume CEPC Chemicals of Emerging Potential Concern CHI Cultural Health Index CCC Criterion Continuous Concentration (US EPA chronic criterion) CCME Canadian Council of Ministers for the Environment CMC Criterion Maximum Concentration (US EPA acute criterion) CRI Cox-Rutherford Index (a measure for stream temperature) Cu Copper DOC Dissolved oxygen DOC Dissolved organic carbon DTA Direct toxicity assessment (ANZECC 2000) EC Emerging contaminant ECR Environmental Compensation Ratio EHMP Ecosystem Health Monitoring Programme EIA Environmental Impact Assessment EPA New Zealand Environmental Protection Authority EPT Ephemeroptera (mayflies), plecoptera (stoneflies), tricoptera (caddisflies): (rivers) ER Ecosystem respiration: (rivers) FC Faecal coliform FMU Freshwater Management Unit GPP Gross primary productivity: (rivers) HRA Health Risk Assessment IBI Index of biological integrity: (fish index for rivers) III Invasive Impact Index: (lakes, macrophytes) LSI LakeSPI Index: (lakes) MAV Maximum Acceptable Value (drinking water terminology) MCC Macrophyte Channel Clogginess (streams and rivers) MCI Macroinvertebrate community index (rivers) Technical aspects of integrating water quality science in the freshwater and coastal environments 173

184 Acronym MPN NEMaR NOF NOM MSP NPS NPS-FM NRWQN NZDWG PAH PAUP Pb PEI PP QIBI QMCI QMRA REC RHA RI SA SAR SDR SEV SOD SoE TAN TDS TLI TPH TV US EPA WER WETT WQC WQI WQO WWTP Zn Definition: (relevant environment) Most Probable Number (microbiological measure) National Environmental Monitoring and Reporting National Objectives Framework Natural Organic Matter Marine Spatial Planning National Policy Statement National Policy Statement for Freshwater Management National River Water Quality Network New Zealand Drinking Water Guidelines Polycyclic aromatic hydrocarbons Proposed Auckland Unitary Plan Lead Periphyton Enrichment Index: (rivers) Priority Pollutants Quantitative index of biological integrity: (fish index for rivers) Quantitative macroinvertebrate community index: (rivers) Quantitative Microbial Risk Assessment River Environment Classification Rapid Habitat Assessment Rotifer index: (lakes) Surface area (macrophytes in streams and rivers) Sediment Accumulation Rate (estuary) Sediment Deposition Rate (rivers) Stream Ecological Valuation Sediment Oxygen Demand State of the Environment total ammoniacal-nitrogen total dissolved solids Trophic level index: (lakes) total petroleum hydrocarbons Trigger value: (rivers and lakes) United States Environmental Protection Agency Water effect ratio Whole Effluent Toxicity Testing Water Quality Criteria Water Quality Index Water Quality Objective Waste Water Treatment Plant Zinc Technical aspects of integrating water quality science in the freshwater and coastal environments 174

185 19.2 Glossary Attribute Term Attribute state Compulsory values Contaminant Transition issue Ecological health Ecological integrity Freshwater Management Unit (FMU) Guideline (water quality) Hardness Limit Definition (reference source) Is a measurable characteristic of fresh water, including physical, chemical and biological properties, which supports particular values (MfE 2014a) Is the level to which an attribute is to be managed for those attributes specified in Appendix 2 of MfE (2014a) Mean the national values relating to ecosystem health and to human health for recreation included in Appendix 1 and for which a nonexhaustive list of attributes is provided in Appendix 2. (MfE 2014a) Biological (e.g., bacterial and viral pathogens) or chemical (e.g., toxicants) introductions capable of producing an adverse effect in a water body. (ANZECC 2000). Relates to a parameter s numeric objective or load which is established in freshwater and its applicability to an estuarine environment. A transition issue may relate to various physico-chemical factors (e.g., ph, metal adsorption) or multiple parameters required for management (e.g., muddiness, light, suspended sediment, nutrients for estuarine macrophytes) and which are affected by the freshwater/estuarine salinity transition. This transition commonly results in marked changes in sediment characteristics and the formation of the estuarine turbidity maxima. Indicates the preferred state of sites that have been modified by human activity, ensuring that their ongoing use does not degrade them for future use. (Karr 1999) The degree to which the physical, chemical and biological components (including composition, structure and process) of an ecosystem and their relationships are present, functioning and maintained close to a reference condition reflecting negligible of minimal anthropogenic impacts. This means full integrity is attained when human actions have little or no influence on sites. This definition distinguishes ecological integrity from ecosystem health, which assesses the state of an ecosystem in terms of the stresses put on it, and its ability to keep providing products and processes for both economic and ecological means. (Schallenberg et al. 2011) Is the water body, multiple water bodies or any part of a water body determined by the regional council as the appropriate spatial scale for setting freshwater objectives and limits and for freshwater accounting and management purposes (MfE 2014a) Numerical concentration limit or narrative statement recommended to support and maintain a designated water use (ANZECC 2000) The concentration of all metallic cations, except those of the alkali metals, present in water. In general, hardness is a measure of the concentration of calcium and magnesium ions in water and is frequently expressed as mg/l calcium carbonate equivalent. (ANZECC 2000) A limit is the maximum amount of resource available, which allows a freshwater objective to be met (MfE 2014a) Technical aspects of integrating water quality science in the freshwater and coastal environments 175

186 Term Definition (reference source) The term limit is defined in the NPS-FM as the maximum amount of resource use available, which allows a freshwater objective to be met. The NPS-FM Implementation Guide expands on the above definition by stating that a limit is a specific quantifiable amount.[1] The NPS-FM Implementation Guide gives an example of a maximum contaminant load for a water quality limit. The Implementation Guide says this would be a common type of limit, but does not suggest that this is the only type of limit. However, it does not give examples of what other types of limits might be. Mahinga kai Mahinga kai generally refers to indigenous freshwater species that have traditionally been used as food, tools, or other resources. Mahinga kai provide food for the people of the rohe and these sites give an indication of the overall health of the catchment. (MfE 2014a) National value Means any value described in Appendix 1. (MfE 2014a) (Management ) Objective Describes the intended environmental outcomes(s) (definition from National Policy Statement for Freshwater Management). Freshwater objectives are set in regional planning documents and describe the desired state of the water body, having taken into account all desired values Pollution The introduction of unwanted components into waters, air or soil, usually as result of human activity; e.g., hot water in rivers, sewage in the sea, oil on land. (ANZECC 2000) Potential conflict Relates to a parameter s numeric objective or load which is established in freshwater and its applicability to an estuarine environment. A potential conflict may occur for that parameter if it is relevant to the values (uses) within the estuary. Some potential conflicts may not occur because of low marine sensitivity (e.g., water nitrate toxicity) or the use cannot occur (e.g., drinking water). The assessment is made without consideration of dilution/dispersion/flushing which may occur in a specific estuary. Reference condition An environmental quality or condition that is defined from as many similar systems as possible and used as a benchmark for determining the environmental quality or condition to be achieved and/or maintained in a particular system of equivalent type. (ANZECC 2000) Secondary contact Means people s contact with fresh water that involves only occasional immersion and includes wading or boating (except boating where there is high likelihood of immersion). (MfE 2014a) Standard (water quality) An objective that is recognised in enforceable environmental control laws of a level of government. State A range in the level of an attribute that may be described as a narrative or numerically. Four different states are specified for attributes (A, B, C or D). The term band, instead of the term state, was previously used in the development of the National Objectives Framework. Target Is a limit which must be met at a defined time in the future. This meaning only applies in the context of over-allocation. (MfE 2014a) Toxicant A chemical capable of producing an adverse response (effect) in a biological system, seriously injuring structure or function or producing death. Examples include pesticides, heavy metals and biotoxins (i.e., domoic acid, ciguatoxin and saxitoxins). (ANZECC 2000) Toxicity The inherent potential or capacity of a material to cause adverse effects in a living organism. Toxins Specific term for biotoxins. Technical aspects of integrating water quality science in the freshwater and coastal environments 176

187 Term Trigger value (TV) Uses Value Freshwater Management Unit (FMU) Water quality criteria Water quality objective Definition (reference source) These are the concentrations (or loads) of the key performance indicators measured for the ecosystem, below which there exists a low risk that adverse biological (ecological) effects will occur. They indicate a risk of impact if exceeded and should trigger some action, either further ecosystem specific investigations or implementation of management/remedial actions. (ANZECC 2000) The uses to for a water body equivalent to Values. a) any national value; and b) includes any value in relation to freshwater, that is not in Appendix 1, which a regional council identifies as appropriate for regional or local circumstances (including any use value). (MfE 2014a) Spatially distinct unit where defined water management policies apply. A FMU may be a catchment, sub-catchment, or group of reaches with similar attributes. Scientific data evaluated to derive the recommended quality of water for various uses. (ANZECC 2000) A numerical concentration limit or narrative statement that has been established to support and protect the designated uses of water at a specified site. It is based on scientific criteria or water quality guidelines but may be modified by other inputs such as social or political constraints. (ANZECC 2000) Technical aspects of integrating water quality science in the freshwater and coastal environments 177

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200 21 Appendices Appendix A: Values and parameters included in this review Appendix B: Numeric environmental management guidelines Appendix C: Other indices Appendix D: National Objectives Framework (NOF) Standards (MfE 2014a) Technical aspects of integrating water quality science in the freshwater and coastal environments 190

201 Appendix A: Values and parameters included in this review The appendices to the Request For Proposal (RFP) included a range of values/objectives and possible parameters which could be included: Appendix 1. Potential Groups of Values/Objectives that could be used (instead of water classes described in Schedule 3 of RMA) 1. Natural State 2. Ecosystem Health 3. Domestic Use 4. Industrial Use 5. Public Water Supply 6. Stock Watering 7. Irrigation 8. Food production and harvest 9. Primary Contact 10. Secondary Contact 11. Aesthetics/Visual amenity 12. Tangata whenua values Te Mana o te Wai (mahinga kai, mauri, wai tapu) 13. Fisheries (Fish spawning, other) Appendix 2. Possible Parameters Temperature ph Dissolved oxygen (rivers) Clarity Turbidity Salinity Sediment/Suspended Solids Total Nitrogen (lakes) Total Phosphorus (lakes) Nitrate toxicity (lakes and rivers) Ammonia Toxicity (Ammoniacal Nitrogen) (lakes and rivers) Nutrients e.g., N, P, ammonia, chlorophyll a, macrophytes, Periphyton (rivers) Microbiological e.g., E.coli, cyanobacteria (planktonic) (lakes and rivers) Heavy metals e.g., copper, zinc, lead, cadmium a Conductivity Others Habitat, MCI, Fish Productivity, River Connectivity, SEV, Lake SPI, Rotifer Index, QIBI, Cultural CHI, Mauri meter Fish IBI a, CCME Water Quality Index a and others. a Strike through and additional parameters (*) indicate changes to the original proposal following the inception workshop. Technical aspects of integrating water quality science in the freshwater and coastal environments 191

202 Appendix B: Numeric environmental management guidelines Table B1: Information location in the ANZECC (2000) guidelines documents Where to find the trigger values in the ANZECC (2000) guidelines Values Aquatic ecosystems: physical and chemical stressors Aquatic ecosystems: sediment quality guidelines Aquatic ecosystems: toxicants Irrigation water supply Livestock water supply Aquaculture a MoH (2008, 2013) b MfE/MoH (2003) Drinking water quality Recreational water quality Environmental values and uses protected by water quality objectives: Table number 3.3.1, and Separate guidelines a All tables in section 4.2 All tables in section 4.3. Detail in section 9.3. All tables in section 9.4 Separate guidelines b Aquatic ecosystems Aquatic foods (cook before eating) Drinking water at point of supply Homestead water supply Irrigation water supply Livestock water supply Aquaculture Primary contact recreation Secondary contact recreation Visual amenity Technical aspects of integrating water quality science in the freshwater and coastal environments 192

203 Table B2: Numeric guidelines for a range of freshwater values. All concentrations µg/l (ppb) unless other units stated Parameter / Components ANZECC protection Ecosystem health thresholds for (ANZECC 2000 unless freshwater and specified) a marine guidelines (% protection) [Alphabetic indicates proposed NOF thresholds] NOF (median, annual maximum/minimum (bracketed)) (mg/l unless stated) Physicochemical "trigger values" (ANZECC) d Human health: Drinking water (NZDWG; MOH 2005) Human health: Consumption Human: Recreation (primary contact) (ANZECC) Human: Recreation (secondary contact) Aesthetic (NZDWG; MOH 2005) Stock water (ANZECC) Irrigation (ANZECC) Aquaculture (ANZECC) ANZECC protection thresholds for marine guidelines (% protection) Marine guideline (concentration) (ANZECC unless indicated) Temperature [A] [B] [C] [D] <3 C (RMA); <2 C (ANZECC 1992) (see text for proposals) C Ranges for various groups. <2 C over 1 hour for change. ph [A] [B] [C] [D] (ANZECC 1992); (US EPA) (see text for proposals) (upland river); (low land river) ; (ANZECC p5-7) (<0.2 units from natural variation) (US EPA) Dissolved oxygen [A] [B] [C] [D] 80-90% saturation (ANZECC 1992) >8.0 (>7.5) ( ) ( ) <5.0 (<4.0) % (upland river); % (low land river) >6.5 (>80% saturation) Various Site-specific for specified areas (US EPA 2000) Clarity <10% change in euphotic depth (lakes, MfE 1994); see Aesthetic for rivers. 0.8 m (upland river); 0.6 m (low land river) Visual Clarity - Black disc (m): 1.6 m; Visual clarity change: <20% or 33% - 50% change for contact recreation (depending on w ater class MfE 1994); <20% change in clarity, <10 points Munsell hue (ANZECC 2000, p5-6). NG (see Aesthetic) Turbidity NG 4.1 NTU (upland river); 5.6 NTU (low land river) (see clarity) 2.5 NTU (see suspended solids) Total suspended solids NG <40 mg/l NG Salinity (chloride) NG 400,000 µg/l 250 mg/l NG? Conductivity (total dissolved solids) 500 µs/cm (ANZECC (1992) µg/l 1000 mg/l <4000 mg/l (species differences) <3 mg/l Total nitrogen Total phosphorus Nitrate nitrogen (toxicity) Nitrate nitrogen (eutrophication) Nitrite nitrogen (toxicity) [A] [B] [C] [D] [A] [B] [C] [D] 99 [A] 95 [B] [C] [D] NG <160 {<300, polymictic} { } { } >750 {>800} µg N/L NG < >50 µg P/L mg NO 3 -N/L - <10 to <295 µg-n/l for cobble streams depending on accrual period 60 (Environment Canada 2016) 1.0 (1.5) 2.4 (3.5) 3.8 (5.6) 6.9 (9.8) >6.9 (>9.8) mg NO 3 -N/L 295 (upland river); 614 µg N/L (low land river) 26 (upland river); 33 µg P/L (low land river) 167 (upland river); 444 µg NO 3 -N/L (low land river) 50 mg NO 3 /L (short-term) 3 mg NO 2 /L (short-term); 0.2 mg NO 2 /L (long-term) Hardness NA 500,000 µg/l 200 mg/l (scale) mg/l (STV); 5 mg/l (LTV) mg/l (STV); 0.05 mg/l (LTV) NG NG <0.1 mg/l NG 10,000 µg NO 3 -N/L 400 mg/l <50 mg/l 45 mg/l (Environment Canada, CCME 2012a,b) 1000 µg NO 2 -N/L 30 mg/l <0.1 mg/l NG NG mg/l NA Technical aspects of integrating water quality science in the freshwater and coastal environments 193

204 Table B2: Cont. Parameter ANZECC protection thresholds for freshwater and marine guidelines (% protection) [Alphabetic indicates proposed NOF thresholds] Ecosystem health (ANZECC 2000 unless specified) a NOF (proposed)(median, annual maximum/minimum (bracketed)) (mg/l unless stated) Physicochemical "trigger values" (ANZECC) d Human health: Drinking water (NZDWG; MOH 2005) Human health: Consumption Human: Recreation (primary contact) (ANZECC) Human: Recreation (secondary contact) Aesthetic (NZDWG; MOH 2005) Stock water (ANZECC) Irrigation (ANZECC) Aquaculture (ANZECC) ANZECC protection thresholds for marine guidelines (% protection) Marine guideline (concentration) (ANZECC unless indicated) Ammoniacal nitrogen Dissolved reactive phosphorus Chlorophyll a 99 [A] 95 [B] [C] [D] [A] [B] [C] [D] µg NH 4 -N/L - <0.03 (<0.05) ( ( ) >1.30 (>2.20) mg NH 4 -N/L <1 to <26 µg P/L for Periphyton cover proposed cobble streams depending on accrual period (Biggs 2000) NG <2 (<10) mg chl-a /m (10-25) 5-12 (25-60) >12 (>60) 10 (upland river); 21 µg NH 4 -N/L (low land river) 9 (upland river); 10 µg P/L (low land river) 10 µg NH 4 -N/L 1.5 mg/l (odour threshold) NG <0.025 (ph >8.0 cold); 0.0? (ph <8.0) mg/l µg NH 4 -N/L <0.1 mg/l NG Macrophytes NG NG Periphyton [A] [B] [C] [D] 30% cover, >2 cm long for filamentous algae (Biggs 2000) <50 mg chl-a /m >200 NA Colour (see Aesthetic) 10 TCU NG Oil & Grease Narrative <0.3 mg/l Narrative NG Microbiological E. coli [A] [B] [C] [D] NG < >1000 E.coli /100 ml Less than one in 100 ml of sample Shellfish standards (FSANZ 2005) <126/100 ml (bathing season median), < /100 ml (single sample depending on extent of contact) (Dept of Health 1992); Beach grading (A-D) based on 95th percentiles. Single sample interpretation: Acceptable (Green) Mode <260/100mL; Alert (Amber) mode /100mL; Action (Red) mode >550/100mL (MfE 2003) (see NOF) NG NG? (see freshw ater) Faecal coliforms NG Shellfish gathering w aters: <14/100 ml (median), <43/100 ml (90th percentile) (MfE 2003) Median: 150 faecal coliform organisms/100 ml (minimum of five samples taken at regular intervals not exceeding one month, w ith four out of five samples containing less than 600 organisms/100 ml); (ANZECC 2000, p5-4) Enterococci NG NG Median: <33/100mL (bathing season), <61-151/100mL (single sample) Dept of Health 1992); Median: 35 enterococci organisms/100 ml (maximum number in any one sample: organisms/100 ml) (ANZECC ) Protozoans NG Pathogenic free-living protozoans should be absent from bodies of fresh w ater. (It is not necessary to analyse w ater for these pathogens unless the temperature is greater than 24 C) (ANZECC 2000) Median: 1000 faecal coliform organisms/100 ml (minimum of five samples taken at regular intervals not exceeding one month, w ith four out of five samples containing less than 4000 organisms/100 ml); (ANZECC 2000, p5-4) Median: 230 enterococci organisms/100 ml (maximum number in any one sample: organisms/100 ml). (ANZECC 2000, p5-4) <100/100 ml (see freshw ater) Acceptable (Green) Mode <140/100mL; Alert (Amber) mode /100mL; Action (Red) mode >280/100mL (MfE 2003) NG Technical aspects of integrating water quality science in the freshwater and coastal environments 194

205 Table B2: Cont. Parameter ANZECC protection thresholds for freshwater and marine guidelines (% protection) [Alphabetic indicates proposed NOF thresholds] Ecosystem health (ANZECC 2000 unless specified) a NOF (proposed)(median, annual maximum/minimum (bracketed)) (mg/l unless stated) Physicochemical "trigger values" (ANZECC) d Human health: Drinking water (NZDWG; MOH 2005) Human health: Consumption Human: Recreation (primary contact) (ANZECC) Human: Recreation (secondary contact) Aesthetic (NZDWG; MOH 2005) Stock water (ANZECC) Irrigation (ANZECC) Aquaculture (ANZECC) ANZECC protection thresholds for marine guidelines (% protection) Marine guideline (concentration) (ANZECC for differing levels of protection unless indicated) Microbiological NG NG Campylobacter Viruses NG No values have been set due to lack of reliable evidence Cyanobacteria (planktonic) Cyanobacteria (benthic) Cyanobacteria (cyanotoxins) Metals Copper [A] [B] [C] [D] [A] [B] [C] [D] [A] [B] [C] [D] Zinc Lead Cadmium (see NOF) <0.5 mm 3 /L biovolume all N/A 0.5-<1.8 potentially toxic ,500 cells/ml (Microcystis) (see NOF) Proposed for future NG (see NOF) Proposed for future Various 2.3 µg/l (microcystin-lr toxicity equivalents) µg/l µg/l µg/l µg/l 2000 µg/l DWG; 1000 µg/l (tainting) NG ,000; 5000 µg/l (tainting) 1000 µg/l 1000 µg/l 400 (sheep) 1000 (cattle) 5000 (pigs) 5000 (poultry) µg/l 5000 (STV); 200 (LTV) µg/l 5000 µg/l 1500 µg/l 20,000 µg/l 5000 (STV); 2000 (LTV) µg/l 10 µg/l 50 µg/l 100 µg/l 5000 (STV); 2000 (LTV) µg/l 4 µg/l DWG 5 µg/l 10 µg/l 50 (STV); 10 (LTV) µg/l Iron 1000 µg/l (US EPA) NG 300 µg/l 300 µg/l 200 µg/l NG 10,000 (STV); 200 (LTV) µg/l Manganese µg/l 50 µg/l 100 µg/l 40 µg/l NG 10,000 (STV); (LTV) µg/l µg/l Aluminium (ph>6.5) µg/l NG 200 µg/l 100 µg/l 5000 µg/l 20,000 (STV); 5000 ( µg/l) µg/l <5 µg/l (hardness dependent) <5 µg/l <1-7 µg/l (hardness dependent) < µg/l (hardness dependent) NG NG NG µg/l µg/l µg/l µg/l <10 µg/l NG <10 µg/l b <30 (ph >6.5) <10 (ph<6.5) µg/l NG Technical aspects of integrating water quality science in the freshwater and coastal environments 195

206 Table B2: Cont. Parameter ANZECC protection thresholds for freshwater and marine guidelines (% protection) [Alphabetic indicates proposed NOF thresholds] Ecosystem health (ANZECC 2000 unless specified) a NOF (proposed)(median, annual maximum/minimum (bracketed)) (mg/l unless stated) Physicochemical "trigger values" (ANZECC) d Human health: Drinking water (NZDWG; MOH 2005) Human health: Consumption Human: Recreation (primary contact) (ANZECC) Human: Recreation (secondary contact) Aesthetic (NZDWG; MOH 2005) Stock water (ANZECC) Irrigation (ANZECC) Aquaculture (ANZECC) ANZECC protection thresholds for marine guidelines (% protection) Marine guideline (concentration) (ANZECC for differing levels of protection unless indicated) Metaloids Arsenic Non-metallic inorganics Arsenic (AsIII); 0.8 (AsV); 24 (AsIII); 13 (AsV); 94 (AsIII); 42 (AsV); 360 (AsIII); 140 (AsV) µg/l b µg/l 10 µg/l µg/l (US EPA; w ater + organism, organism only) 50 µg/l 500 µg/l 2000 (STV); 100 (LTV) µg/l Footnotes: a: Red highlight indicates ANZECC guideline normally used b: Parameters due for updating with current ANZECC revisions c: Guidelines are for unionised hydrogen sulphide d: ANZECC (2000) physico-chemical trigger values are benchmark values from river monitoring and do not represent thresholds for adverse biological effects (see text). Abbreviations: EC = Environment Canada guideline; DWG = drinking water guideline; May require reference site for comparative assessment. See text for discussion. NG = no numeric guidelines; NA = not applicable; LTV = long-term trigger value; STV = short-term trigger value. 50 µg/l 36 µg/l (US EPA) 10 µg/l 1000 µg/l 5000 µg/l 500 (LTV) µg/l NG Fluoride NG 1500 µg/l 2000 µg/l 42,000 (STV); 1000 (LTV) µg/l Hydrogen sulphide c µg/l <200 µg/l 5 mg/l (total F) NG 50 µg/l NG NG <1 µg/l NG (use FW) Macroinvertebrate NA (see text for proposals) NA community index (MCI) Fish IBI NA NA OIBI NA NA River connectivity NA NA Lake SPI NA NA Habitat NA Stream Ecological NA NA Valuation (SEV) Rotifer index NA NA CCME water quality index NA NA Technical aspects of integrating water quality science in the freshwater and coastal environments 196

207 Appendix C: Other indices Table C1: Other potential indices. Usefulness ranking 2 (see Section 15 for priority ranked indices). Indicator type Indicator name Habitat Description Advantages Disadvantages Usefulness (1=very useful, 5=not useful) Functional Functional Gross Primary Productivity (GPP) Ecosystem Respiration (ER) streams streams The balance between GPP and ER shows whether in-stream or terrestrial energy sources are more important in fuelling the stream food web. The balance between GPP and ER shows whether in-stream or terrestrial energy sources are more important in fuelling the stream food web. Functional Organic Matter Processing streams Measures the capacity of stream microbes and macrofauna to make use of incoming terrestrial food sources. Fish % alien lakes and streams The proportion of fish (individuals) that are non-native. Phytoplankton Cyanobacterial blooms lakes.presence/absence of blooms, monitored at frequent intervals during warm stable weather Combined indices Combined indices Index of biological integrity (IBI) Average score per metric (ASPM) streams streams Combines five macroinvertebrate indices (QMCI, %EPT, %shredders, total richness, EPT richness, community loss index) Combines three macroinvertebrate indices (EPT richness, %EPT abundance and MCI) into a single score Adequate characterisation of ecosystems requires information on both structure and function. GPP complements "structural" measures. Already being measured at some sites. Adequate characterisation of ecosystems requires information on both structure and function. GPP complements "structural" measures. Already being measured at some sites. Adequate characterisation of ecosystems requires information on both structure and function. Organic matter processing complements "structural" measures. Very useful for lakes: lake instability is highly correlated with the presence of pest fish. For streams, may be easy to calculate if quantitative fish surveys are already being done. May be useful complement to Fish IBI Rapid, low-cost May be hard to distinguish natural variability from effects of human impacts. Further work needed to interpret results. May be hard to distinguish natural variability from effects of human impacts. Further work needed to interpret results. May be hard to distinguish natural variability from effects of human impacts. Further work needed to interpret results. In lakes, pest fish surveys may be very onerous. "Catchability of fish differs between species in ways that are unrelated to the relative abundance of the species in the lake. Not currently used as an index in NZ lakes. Species identification not included. Only certain species are toxic. Condition bands clearly defined. Requires fully quantitative Multimetrics integrate a wider range of macroinvertebrate data responses to environmental stressors than a single index does. Scaled to "best possible" reference condition. Can be calculated from existing macroinvertebrate data, provided it is quantitative. Distinguishes low and moderate impact sites better, and is more stable over time, than its component variables. Developed for the Waikato. Needs to be validated for Auckland. Cost Feasibility Include or exclude? 2 high (equipment cost) 2 high (equipment cost) 2 high (labourintensive) difficult difficult 2 high (labourintensive) for lakes. lakes; medium difficult for Low for streams if for streams quantitative surveys already being done future; include at some sites future; include at some sites Main reason for including or excluding Already being measured at some sites Already being measured at some sites difficult exclude Interpretation of results is difficult consider May be easy to calculate for streams. Very useful for lakes if difficulties can be resolved. 2 low easy include Indicator of eutrophication. Toxic blooms are relevant to human health and recreation. Simple, low cost. 2 medium if need to change macroinvertebrate protocols 2 medium if need to change macroinvertebrate protocols easy consider Consider whether simplicity of the combined index justifies extra cost o fully quantitative macroinvertebrate protocols easy consider Consider whether simplicity of the combined index justifies extra cost o fully quantitative macroinvertebrate protocols Requires reference site? no no no no no References Davies-Colley et al. (2012a); Young et al Davies-Colley et al. (2012a); Young et al Davies-Colley et al. (2012a); Young et al Davies-Colley et al. (2012a); /ehmp/filelibrary/freshw_methodsfishi.pd f Davies-Colley et al. (2012a) yes Quinn et al. (2004) no Collier (2008) Table C2: Other potential indices. Usefulness ranking 3 and greater (see Section 15 for priority ranked indices). Technical aspects of integrating water quality science in the freshwater and coastal environments 197

208 Indicator type Indicator name Habitat Description Advantages Disadvantages Usefulness (1=very useful, 5=not useful) Functional Nutrient processing streams and lakes Macroinvertebrate Indices The ratio of nitrogen stable isotopes (15N:14N) in aquatic plants and algae can show changes to the natural cycling of nitrogen in streams due to diffuse or point-source pollution. Species traits streams macroinvertebrate data are analysed in terms of characteristics (e.g. mode of movement, number of generations per year, breathing mode) rather than species. Microinvertebrates Rotifer index (RI) lakes The composition of rotifer species in a lake indicates the trophic state of the lake. Fish Periphyton native observed vs. expected Periphyton Enrichment Index (PEI) lakes and streams streams The number of native fish species present at a site as a proportion of the number expected. visual survey of stream bed to identify different periphyton growth forms. Percent cover of the different forms are multiplied by a weighting factor and summed to give PEI. Adequate characterisation of ecosystems requires information on both structure and function.. Complements "structural" measures. Used routinely for stream monitoring in South East Queensland. Can be calculated from existing macroinvertebrate data. Indicates changes in biological function, not just in community structure. Potentially able to diagnose types of stressors at a site. Ecologically relevant for lakes. For streams, may be easy to calculate if quantitative fish surveys are already being done. May be useful complement to Fish IBI Periphyton is a sensitive indicator of nutrient enrichment and (lack of) shading. Field method rapid. No laboratory analysis required. Robust scientific basis. Not yet developed for New Zealand. May be confounded by nitrogen inputs from legumes (e.g. gorse) and marine influences Species trait database for New Zealand needs further development and testing. Use as a diagnostic tool also needs further development May not give much information additional to the Lake Trophic Level Index (TLI). May require specialist identification skills. In lakes, fish surveys may be very onerous; catchability of fish differs between species in ways that are unrelated to the relative abundance of the species in the lake. Not currently used as an index in NZ lakes. May require new models to predict "expected" native fish. For hard-bottomed streams only. Most Auckland streams are softbottomed. Cost Feasibility Include or exclude? Main reason for including or excluding? high difficult exclude Interpretation of results is difficult Requires reference site? no References Davies-Colley et al. (2012a); /ehmp/filelibrary/freshw_methodsnutrient c.pdf 3 low easy exclude Needs further development no Phillips and Reid (2012)?? difficult exclude Needs further development. Unclear if provides additional information.? high (labourintensive) for lakes. lakes; medium difficult for Low for streams if for streams quantitative surveys already being done consider may be easy to calculate for streams. Very useful for lakes if difficulties can be resolved. 5 low easy exclude Not relevant in Auckland. Macrophytes are more relevant than periphyton as biological indicators. no Duggan et al. (2001) maybe no Davies-Colley et al. (2012a); /ehmp/filelibrary/freshw_methodsfishi.pd f Davies-Colley et al. (2012a); Kilroy et al Technical aspects of integrating water quality science in the freshwater and coastal environments 198

209 Appendix D: National Objectives Framework (NOF) Standards (MfE 2014a) Table D1 Phytoplankton (Chlorophyll a) for lakes MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 199

210 Table D2 Total nitrogen for lakes (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 200

211 Table D3 Total phosphorus for lakes (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 201

212 Table D4 Periphyton for rivers (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 202

213 Table D5 Nitrate for rivers (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 203

214 Table D6 Ammonia for lakes and rivers (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 204

215 Table D7 Dissolved oxygen for rivers below point source discharges (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 205

216 Table D8 Faecal indicators (E. coli) for lakes and rivers (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 206

217 Table D9 Cyanobacteria for lakes and lake-fed rivers (MfE 2014a). Technical aspects of integrating water quality science in the freshwater and coastal environments 207