WATER QUALITY STATUS AND TREND MONITORING SYSTEM FOR THE CLARK FORK-PEND OREILLE WATERSHED

Transcription

1 WATER QUALITY STATUS AND TREND MONITORING SYSTEM FOR THE CLARK FORK-PEND OREILLE WATERSHED Summary Monitoring Report 3 Prepared for: TRI-STATE WATER QUALITY COUNCIL Diane Williams, Executive Director 37 North Second Avenue, Suite 12 Sandpoint, ID Prepared by: LAND & WATER CONSULTING, INC. PO Box 824 Missoula, MT 87 April 4 Project # Cedar Street P.O. Box 824 Missoula, Montana 87 Tel (46) info@landandwater.net Fax (46) 721-3

2 TABLE OF CONTENTS EXECUTIVE SUMMARY... i 1. INTRODUCTION Background History Monitoring Program Goals Project Description Sampling Methods Field Constituents - Clark Fork and Pend Oreille Rivers Nutrients and Metals Clark Fork and Pend Oreille Rivers Periphyton Clark Fork River and Pend Oreille Lake Secchi Depth Pend Oreille Lake Analytical Methods Statistical Methods WATER QUALITY STATISTICS Algal Nutrients Spatial Comparison Total Nitrogen Total Soluble Inorganic Nitrogen Total Phosphorus Soluble Reactive Phosphorus Heavy Metals Spatial Comparison Total Recoverable Copper Total Recoverable Zinc Total Recoverable Cadmium Dissolved Metals Field Constituents Spatial Comparison Temperature ph Conductivity Dissolved Oxygen Turbidity Summer Nutrient Levels Summer Boxplots Summer Summary Statistics PERIPHYTON STATISTICS Periphyton Temporal Comparison Clark Fork River Pend Oreille Lake Periphyton Spatial Comparison Clark Fork River Pend Oreille Lake Secchi Depth REFERENCES...18

3 FIGURES Figure 1-1 Figure 3-1 Figure 3-2 Figure 3-3 Figure 3-4 Figure 3- Figure 3-6 Figure 3-7 Boxplot Construction Clark Fork at Deer Lodge chlorophyll a values compared to instream target levels, 18-3 Clark Fork above Little Blackfoot chlorophyll a values compared to instream target levels, 18-3 Clark Fork at Bonita chlorophyll a values compared to instream target levels, 18-3 Clark Fork above Missoula chlorophyll a values compared to instream target levels, 18-3 Clark Fork below Missoula chlorophyll a values compared to instream target levels, 18-3 Clark Fork at Huson chlorophyll a values compared to instream target levels, 18-3 Clark Fork above Flathead chlorophyll a values compared to instream target levels, 18-3 TABLES Table 1-1 Table 1-2 Table 1-3 Table 2-1 Monitoring Locations, Rationale, and Sampling Frequency Sampling Protocol Analytical Methods and Detection Limits Summer Sample Nutrient Target Compliance APPENDICES Appendix A Water Quality Monitoring Stations and Sampling Frequency/Figures TABLE 1 WATER QUALITY MONITORING STATIONS AND SAMPLING FREQUENCY, 3 FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE Appendix B Appendix C Appendix D Appendix E Appendix F Appendix G Appendix H Appendix I PROJECT STUDY AREA WATERSHED BOUNDARIES NUTRIENTS AND METALS MONITORING SITES ADDITIONAL SUMMER NUTRIENT MONITORING SITES PERIPHYTON DENSITY MONITORING SITES 3 Water Quality Data Spatial Boxplots 3 Water Quality Data Summary Statistics Tables 3 Summer Water Quality Data Spatial Boxplots 3 Summer Water Quality Data Summary Statistics Tables 3 Clark Fork River Periphyton Boxplots 3 Pend Oreille Lake Periphyton Boxplots 3 Pend Oreille Lake Secchi Depth Boxplots Contributors to the Tri-State Water Quality Council

4 1. INTRODUCTION 1.1 Background History The mission of the Tri-State Water Quality Council has been to develop a management strategy to restore and protect designated water uses within the Clark Fork-Pend Oreille Basin. The Tri- State Water Quality Council s Clark Fork-Pend Oreille watershed water quality monitoring program was begun in 18 and employs a statistically-based sampling design derived from an analysis of previous nutrient and periphyton data collected for the watershed by the state agencies. Through this design approach, sampling frequencies and monitoring locations have been optimized to provide reliable information for watershed management decision-making while minimizing operational costs. The 3-7 monitoring program represents the second five-year operational period of the Tri-State Water Quality Council s monitoring program. The initial five-year monitoring period (18-2), together with the preexisting agency data, provided the basis for a recently completed statistical analysis of water quality time trends in the Clark Fork-Pend Oreille Basin (Land & Water, 3a). The results of this analysis will be used to further optimize the 3-7 program Monitoring Program Goals The Tri-State Water Quality Council s Water Quality Monitoring Committee has established seven primary monitoring goals for the Clark Fork-Pend Oreille Watershed, which conform to specific watershed management goals articulated in a tri-state management plan (EPA 13). These monitoring goals include: 1) Evaluating time trends in nutrient concentrations in the mainstem Clark Fork River and selected tributaries; 2) evaluating time trends for algal standing crops in the Clark Fork River; 3) monitoring compliance with established summer nutrient concentration target levels in the Clark Fork River; 4) estimating nutrient loading rates to Pend Oreille Lake from the Clark Fork River; ) evaluating time trends for algal standing crops in near-shore areas of Pend Oreille Lake; 6) evaluating time trends for Secchi depth in Pend Oreille Lake; and 7) evaluating time trends for nutrient concentrations in the Pend Oreille River. 1.2 Project Description The study area includes 22 monitoring locations on the Clark Fork River, selected tributaries, Pend Oreille Lake, and the Pend Oreille River within the Clark Fork-Pend Oreille watershed of western Montana, northern Idaho and northeastern Washington (Appendix A). The locations selected for water quality monitoring provide distributed spatial coverage for evaluating the effects of point and non-point pollution sources, and the influences of major population centers and tributary inflows. This design provides for a cost effective and reasonably sensitive 1

5 assessment of nutrient and metals inputs throughout the basin. A summary of monitoring locations, their rationale, and associated sampling frequencies are provided in Table 1-1. Table 1-1. Station STORET ID Monitoring Locations, Rationale, and Sampling Frequency Name Rationale SI Silver Bow Creek at Opportunity below mixing zone for Butte WWTP S CL2 Clark Fork below Warm Springs Creek 326CL1 Clark Fork at Deer Lodge 3726CL1 Clark Fork above Little Blackfoot River 12 31CL1 Clark Fork at Bonita CL1 Clark Fork above Missoula upstream control site, start of Clark Fork River upstream control site, upper river indicator site below mixing zone for Deer Lodge WWTP upper river site, between significant tributaries below Blackfoot drainage, control site for Missoula Sampling Frequency S P, S P, S P, S P, S CL1 Clark Fork below Missoula (Shuffields) below mixing zone for Missoula WWTP P, S CL1 Clark Fork at Huson lower river site, downstream of Missoula P, S 2 47CL1 Clark Fork above Flathead TH1 Thompson River near mouth 28* CL1 Clark Fork below Thompson Falls 2* 43CL1 Clark Fork at Noxon Bridge 3* 38CL1 Clark Fork below Cabinet Gorge Dam lower river site, upstream control for the Flathead River lower river tributary, sponsored on annual basis by Plum Creek lower river site, downstream of Flathead River and TF WWTP lower river site, reflects reservoir influence estimation of nutrient loading to Pend Oreille Lake Pend Oreille River at Newport, WA represents outflow of Pend Oreille Lake N12 Pend Oreille River at Metaline Falls, WA Pend Oreille Lake: Kootenai Pend Oreille Lake: Springy Point Pend Oreille Lake: Sunnyside downstream control site near-shore site, indicator of near-shore nutrient loading near Sandpoint and outflow of Pend Oreille Lake near-shore site, indicator of near-shore nutrient loading Pend Oreille Lake: Trestle Creek near-shore site, near mouth of Pack River P Pend Oreille Lake: Bayview Pend Oreille Lake: Hope Pend Oreille Lake: Granite Point N12 = Nutrient and field constituents, 12 monthly samples NM12 = Nutrient, metal and field constituents, 12 monthly samples NM18 = Nutrient, metal and field constituents, 12 monthly samples and 6 peak flow samples P = Periphyton, replicates per site, August and September S = Summer nutrient and field constituents, samples during 3 weeks in summer SD = Secchi Depth, 12 monthly samples (if available) * These sites sponsored by Avista Corp., pursuant to 41 certification requirement open water site, south end of Pend Oreille Lake near-shore site, over shallow north end of Pend Oreille Lake open water site, over deepest portion of Pend Oreille Lake P, S N12 NM12 NM12 NM18 N12 P P P P, SD SD SD 2

6 Currently, the 3-7 program includes a basic monitoring component and several annual or periodic rotational add-on elements. The basic program consists of the highest priorities for annual monitoring, while the add-ons represent options for additional monitoring that are contingent on annual funding availability. The 3 program included each of the tasks described below, which constitute the basic monitoring program: 1. monthly collection of nutrient and heavy metals samples and field constituents at three Clark Fork River sites, monthly collection of nutrient samples and field constituents at one Thompson River site and two Pend Oreille River sites (April December for Clark Fork and Thompson River sites, January December for Pend Oreille River sites); 2 summer collection of periphyton standing crop samples at seven Clark Fork River sites (August and September); 3. summer collection of nutrient samples and field constituents at nine Clark Fork River sites ( samples over 3 months); 4. collection of nutrient and heavy metals samples at the Clark Fork River below Cabinet Gorge Dam during spring peak flow (six samples over a one-month period, May to June);. summer collection of periphyton standing crop samples at five Pend Oreille Lake sites (September); and 6. monthly Secchi depth readings at three Pend Oreille Lake sites. Nutrient constituents included: total phosphorus (TP), total Kjeldahl nitrogen (TKN) or total persulfate nitrogen (TPN, Washington sites only), nitrate + nitrite nitrogen (NO 2 +NO 3 -N), total ammonia nitrogen (NH 3 +NH 4 -N), and soluble reactive phosphorus (SRP). Heavy metal constituents included total recoverable copper (Cu) and total recoverable zinc (Zn). Two Clark Fork River sites (at Noxon and below Cabinet Gorge Dam) were also sampled for total recoverable cadmium (Cd), dissolved copper (diss Cu), dissolved zinc (diss Zn), and dissolved cadmium (diss Cd). Values for total nitrogen (TN) and total soluble inorganic nitrogen (TSIN) were calculated as follows: T TKN plus NO 2 +NO 3 -N TSI NO 2 +NO 3 -N plus NH 3 +NH 4 -N Field constituents included: water temperature ( C), dissolved oxygen (mg/l), ph (standard units), redox potential (mv), specific conductance (µs/cm), total dissolved solids (mg/l), and turbidity (NTU). Stream flow (instantaneous, cubic feet per second (cfs)) and river stage (ft) were also recorded where gauging stations were available. Periphyton samples from natural substrates were analyzed for chlorophyll a (mg/m 2 ) and ashfree dry weight (g/m 2 ). Secchi depth was recorded in meters (m). This report provides a brief summary of water quality and algae data collected during the 3 calendar year. No detailed study was undertaken for analysis of time trends in water quality, nor were statistical comparisons made of water quality between stations. These types of detailed analyses are conducted once every five years on a complete five-year data set. The 3 calendar year monitoring data will be evaluated fore time trends together with 4-7 data during 8. 3

7 1.3 Sampling Methods Field Constituents Clark Fork and Pend Oreille Rivers Field variables measured in the Clark Fork and Pend Oreille rivers using a hand-held water quality probe included water temperature ( C), dissolved oxygen (mg/l), ph (standard units), redox (mv), conductivity (µs/cm), and total dissolved solids (mg/l. Turbidity (NTU) levels were measured using a portable turbidimeter Nutrients and Metals Clark Fork and Pend Oreille Rivers Water samples for total phosphorus (TP), total Kjeldahl nitrogen (TKN), total persulfate nitrogen (TPN), nitrate plus nitrite-nitrogen (NO 2 NO 3 ), total ammonia-nitrogen (NH 4 ), soluble reactive phosphorus (SRP), total recoverable copper (Cu), and total recoverable zinc (Zn) were collected using a grab sampling technique by wading in a well-mixed portion of the river. Samples were taken in the upstream direction to avoid entrainment of sediment disturbed by wading. Water samples for TP, TKN, Cu, and Zn were collected directly in acid washed, wide-mouthed polyethylene bottles. Bottles were rinsed twice with native water (or filtered native water) prior to sampling. During sampling, the sample bottle was positioned to face upstream and was drawn through the water column once, carefully avoiding disturbance of bottom sediments. Samples were acidified to a ph of less than 2 by adding concentrated sulfuric acid (H 2 SO 4 ) for nutrient samples and concentrated nitric acid (HNO 3 ) for metal samples. Water for soluble nitrogen constituents (NO 2+ NO 3 and NH 4 ) were filtered in the field through a.4 µm filter into acid-washed polyethylene bottles. A small volume of filtrate (3- ml) was discarded before the sample was collected. Nutrient samples (NO 2 NO 3 and NH 4 ) were frozen or acidified to a ph of less than 2 with concentrated sulfuric acid. Soluble reactive phosphorus (SRP) samples were filtered into polyethylene bottles, but were not preserved. SRP samples were cooled to 4 C or less, or frozen. Samples were clearly labeled with a waterproof marker or pre-printed labels. Label information included the site identification number, date and time, sample type, preservative, and sampler s initials. Each bottle was recorded on a chain-of-custody form before leaving the site. All samples were stored in coolers and chilled to 4 C or less (or frozen for SRP) for transport to the lab. A summary of sampling protocols used during 3 is provided in Table 1-2. Table 1-2. Sampling Protocol Constituent Sample Volume Container Preservation Holding Time TP and TKN 2 ml Acid-washed polyethylene H 2 SO 4, cool to 4 C 28 days Cu and Zn 2 ml Acid-washed polyethylene HNO 3 6 months NO 2 NO 3 and NH 4 2 ml Acid-washed Filter, add H 2 SO 4 and cool to polyethylene 4 C, or freeze 28 days SRP 2 ml Acid-washed polyethylene Filter, cool to 4 C or freeze 48 hours 4

8 1.3.3 Periphyton Clark Fork River and Pend Oreille Lake Two types of periphyton samples were collected: hoop samples (a bulk sampling method) and template samples (a rock scraping method). Hoop samples were collected for filamentous green algae (Cladophora) dominated sites (sites above Missoula) and template samples were collected for diatom dominated sites (sites below Missoula). Periphyton samples on Pend Oreille Lake were taken using the template method. Both chlorophyll a and ash-free dry weight (AFDW) were measured from the hoop and template samples. Clark Fork River periphyton samples were collected on two separate sampling events, once in August and again in September, in an attempt to document peak algal standing crops. Pend Oreille Lake periphyton samples were collected in September Secchi Depth Pend Oreille Lake For Secchi depth monitoring, a standard cm Secchi disc was used. Secchi depth readings were taken on the side of the boat with the least amount of surface roughness. Water transparency was evaluated by lowering the Secchi disc over the side of the boat until the markings were no longer visible. The depth was read after the disc was lowered past the extinction point, and then raised until just visible. Depth was recorded in meters. The sampler also noted time of day, weather, water surface conditions, and any other variables that may have affected the reading. 1.4 Analytical Methods State-certified laboratories, including the Montana Department of Public Health and Human Services chemistry laboratory, the Missoula wastewater treatment plant laboratory, and the Washington Department of Ecology Manchester laboratory performed all nutrient and metals analyses using standard methods. The University of Montana biology laboratory performed the periphyton sample analyses. The analytical methods listed in Table 1-3 represent standard accepted procedures. Details regarding these methods are not included in this document but are described in Standard Methods for the Examination of Water and Wastewater, th Ed (APHA 1) and various EPA documents. Table 1-3. Analytical Methods and Detection Limits Analyte Method Detection Limit Total Phosphorus (TP) EPA µg/l Total Kjeldahl Nitrogen (TKN) EPA 31.2 µg/l Nitrate + Nitrite-Nitrogen (NO 2 NO 3 ) EPA 33.2 µg/l Total Ammonia-Nitrogen (NH 4 ) EPA 3.1 µg/l Soluble Reactive Phosphorus (SRP) EPA µg/l Total Recoverable Copper (Cu) EPA.7 1 µg/l Total Recoverable Zinc (Zn) EPA.7. µg/l

9 1. Statistical Methods This report includes summary statistics and boxplots for visual comparisons of water quality. Summary statistics include median, mean, minimum, maximum, standard deviation, and variance. Boxplots compare water quality and algae data from different monitoring station locations (i.e. spatial comparison) or at the same station for different sampling years (i.e. temporal comparison). The shapes of the boxplots are based on median, interquartile, and extreme values of the data. The box encloses the interquartile range, which contains the middle percent of the values. The median value is displayed as the centerline of the box. The top and bottom whiskers display the maximum and minimum observed values, excluding outliers and extreme values. Outliers, defined as values that are 1. to 3 times greater than or less than values in the interquartile range, are displayed as circles ( ). Extreme values, or those more than 3 times the values in the interquartile range, are displayed with an asterisk ( * ). The boxplot construction is shown graphically in Figure 1-1. Figure 1-1. Boxplot Construction 6

10 2. WATER QUALITY STATISTICS 2.1 Algal Nutrients Spatial Comparison Nutrients concentrations tend to vary spatially throughout the Clark Fork-Pend Oreille watershed. Boxplots were used to provide a visual comparison of spatial patterns in nutrient concentrations during 3 (Appendix B). Summary statistics including mean, median, minimum, maximum, standard deviation, and variance values, as well as the number of samples are provided in Appendix C. For boxplot presentations, stations were ordered (left to right) in the upstream to downstream direction Total Nitrogen Median total nitrogen (TN) concentrations were highest in the Clark Fork River below Thompson Falls Dam (. mg/l) and decreased in a downstream direction (. mg/l in the Pend Oreille River at Metaline Falls). Median TN at the Thompson River site (.1 mg/l) was lower than at the three Clark Fork River sites, but slightly higher than the Pend Oreille River sites. The Clark Fork River site below Cabinet Gorge Dam yielded the lowest median TN concentration of the three Clark Fork sites (.1 mg/l), yet all three sites differed only very slightly (.1. mg/l) Total Soluble Inorganic Nitrogen Median total soluble inorganic nitrogen (TSIN) concentrations were lowest in the Thompson River (.1 mg/l). TSIN concentrations tended to increase in the Clark Fork River from below Thompson Falls Dam (.378 mg/l) downstream to the Clark Fork River below Cabinet Gorge Dam (.844 mg/l). Pend Oreille River sites at Newport and Metaline Falls (.14 mg/l and. mg/l respectively) showed TSIN concentrations that were lower than either the Thompson River or the Clark Fork River sites Total Phosphorous Median total phosphorus (TP) concentrations were lowest in the Thompson River (.67 mg/l) and in the Clark Fork River below Thompson Falls Dam (.62 mg/l) and increased at downstream Clark Fork River sites, peaking at the site below Cabinet Gorge Dam (.12 mg/l). Median TP concentrations in the Pend Oreille River (. mg/l at Newport and.8 at Metaline Falls) were comparable to those measured at the lower Clark Fork River sites Soluble Reactive Phosphorus Median soluble reactive phosphorus (SRP) concentrations fluctuated significantly throughout the lower watershed. The highest median concentration in 3 occurred in the Thompson River (.32 mg/l), while the lowest median TN occurred at the Clark Fork River site below Cabinet Gorge Dam (<.1 mg/l). Median concentrations in the Pend Oreille River were higher than in the Clark Fork River below Cabinet Gorge Dam, but it should be noted that detection limits were higher for the Pend Oreille River sites (.3 mg/l) than for the Clark Fork sites (.1 mg/l) due to different analytical laboratories. 7

11 2.2 Heavy Metals Spatial Comparison Total Recoverable Copper Median total recoverable copper (Cu) concentrations were below detection (<.1 mg/l) in the Thompson River site and in the Clark Fork at sites below Thompson Falls Dam and at the Noxon Bridge. No samples taken from the Thompson River produced results above the analytical detection limit (.1 mg/l). The median copper concentration in the Clark Fork River below Cabinet Gorge Dam fell at the detection limit of.1 mg/l Total Recoverable Zinc Median concentrations of total recoverable zinc (Zn) fluctuated throughout the lower watershed. The Thompson River site did not produce any analyses above the analytical detection limit (. mg/l). The three lower Clark Fork River sites exhibited varying median concentrations ranging from.22 mg/l below Thompson Falls Dam, to.6 mg/l at the Noxon Bridge, to. mg/l below Cabinet Gorge Dam). Higher concentrations of total recoverable zinc were measured in samples collected on October 1, 3 at all three lower Clark Fork River sites (.4 mg/l below Thompson Falls,.73 mg/l at Noxon, and.774 mg/l below Cabinet Gorge Dam). It should be noted that the equipment blank also detected a high concentration of TR zinc during this sampling run (.6 mg/l), so values recorded on this date should be viewed with suspicion and are likely erroneous Total Recoverable Cadmium Total recoverable cadmium (Cd) samples were collected at lower Clark Fork River sites at Noxon Bridge and below Cabinet Gorge Dam in 3. All samples from both sites were below the analytical detection limit of.1 mg/l during Dissolved Metals Dissolved metals samples were collected at two sites in 3, the Clark Fork River at Noxon Bridge and below Cabinet Gorge Dam. Samples were analyzed for dissolved copper, dissolved zinc, and dissolved cadmium at these locations. Median dissolved copper concentrations were below the analytical detection limit at Noxon Bridge (<.1 mg/l), and at the detection limit below Cabinet Gorge Dam (.1 mg/l). Median dissolved zinc concentrations were.6 mg/l at Noxon, and. mg/l below Cabinet Gorge Dam. Median dissolved cadmium concentrations were below the analytical detection limit (<.1 mg/l) at both sites in Field Constituents Spatial Comparison Temperature Median stream temperature increased from a low of 8.4 o C in the Thompson River to a high of 14.4 o C in the Clark Fork River below Cabinet Gorge Dam. The Pend Oreille River sites (7.6 o C at Newport and 8. o C at Metaline Falls) were comparable to the Thompson River. However, 8

12 these sites were sampled three additional times in early 3 and this fact may have skewed the median values ph Median ph values were lowest in the Thompson River (7.1) and increased steadily downstream to the Pend Oreille River at Metaline Falls (8.1). ph often increases from morning to evening as plants absorb carbon dioxide during photosynthesis. It is likely that at least some of the between station differences in ph was due to diurnal variations and the upstream to downstream sampling schedule Conductivity Conductivity, an indirect measure of dissolved ion concentrations, was lowest in the Pend Oreille River at Newport and Metaline Falls (1 and 11 µs/cm, respectively). The Thompson River site exhibited a lower median conductivity (17 µs/cm) than the Clark Fork River sites, which varied only slightly (12 µs/cm below Thompson Falls versus 1 µs/cm below Cabinet Gorge Dam) Dissolved Oxygen Median dissolved oxygen concentrations (DO) in 3 were highest at the Thompson River site (12. mg/l) and lowest in the Clark Fork River at the Noxon Bridge (.4 mg/l). Median DO at Pend Oreille River sites (11. and 11.1 mg/l at Newport and Metaline Falls, respectively) was intermediate between the Thompson River and the Clark Fork River sites. Differences in dissolved oxygen concentrations between sampling sites was also probably affected to some degree by sampling times of day and diurnal fluctuations like was suggested for ph Turbidity Median turbidity was lowest at the Thompson River site (1.3 NTU). The highest median turbidity was measured in the Clark Fork River at the sites below Thompson Falls Dam and at the Noxon Bridge (1. NTU), and values decreased somewhat downstream in the Pend Oreille River at Metaline Falls (1.6 NTU). 2.4 Summer Nutrient Levels Intensive summer nutrient monitoring to evaluate compliance with the established instream target concentrations was conducted at one station on Silver Bow Creek and at eight Clark Fork River stations (Appendix A, Figure 4). The following stations were each sampled ten times beginning in May and continuing through September by Missoula wastewater treatment plant personnel: Silver Bow Creek at Opportunity, Clark Fork River below Warm Springs Creek, Clark Fork River at Deer Lodge, Clark Fork River above the Little Blackfoot River, Clark Fork River at Bonita, Clark Fork River above Missoula, Clark Fork River below Missoula, Clark Fork River at Huson, and Clark Fork River above the Flathead River.

13 The following Clark Fork Basin nutrient targets were developed by the Tri-State Water Quality Council and subsequently adopted as water quality standards by the State of Montana (ARM ): Total nitrogen Clark Fork River (headwaters to Flathead River) 3 µg/l Total phosphorous Clark Fork River (headwaters to Missoula) µg/l Total phosphorous Clark Fork River (Missoula to Flathead River) 3 µg/l The Tri-State Council has established secondary target values for soluble inorganic forms of nitrogen and phosphorus in the Clark Fork River, as follows: Total soluble inorganic nitrogen 3 µg/l Soluble reactive phosphorus 6 µg/l Summer Boxplots Spatial comparisons of summer nutrient concentrations in Silver Bow Creek and the Clark Fork River are presented using statistical boxplots (Appendix D). Where appropriate, boxplots are displayed on two scales to better display the data. The relevant target values are shown as horizontal lines, where these are available. The total nitrogen (TN) boxplots show that five stations had median values exceeding the target level (3 µg/l) in 3, including Silver Bow Creek at Opportunity (23 µg/l) and the Clark Fork River at Deer Lodge (27 µg/l), above the Little Blackfoot River (372 µg/l), at Bonita (3 µg/l), and below Missoula (322 µg/l). Median summer TN was highest at the Silver Bow Creek site, and generally decreased in a downstream direction, although increases were noted at Deer Lodge and below Missoula. The lowest median summer TN concentration was observed in the Clark Fork River above the Flathead River confluence (16 µg/l). Median summer total phosphorus (TP) concentrations in the Clark Fork River above Missoula exceeded the µg/l target at three sites in 3, including Silver Bow Creek at Opportunity (182 µg/l) and the Clark Fork River sites above the Little Blackfoot River (26 µg/l) and at Bonita (3 µg/l). Median summer TP in the Clark Fork River increased from below Warm Springs Creek to a peak at the site below Missoula, although a decrease occurred between Bonita and the site above Missoula. As was observed for TN, the lowest median summer TP concentration was observed in the Clark Fork River above the Flathead River confluence ( µg/l). Median summer total soluble inorganic nitrogen (TSIN) concentrations in 3 were well above the target value of 3 µg/l at each of four stations. Silver Bow Creek at Opportunity had the highest median value (1244 µg/l). The Clark Fork stations at Deer Lodge (14 µg/l), below Missoula (86 µg/l), and at Huson (6 µg/l) also exceeded the instream target. The Clark Fork River sites above the Little Blackfoot River and above Missoula had the lowest median summer TSIN values at 7. µg/l.

14 Median summer soluble reactive phosphorus (SRP) concentrations exceeded the target value of 6 µg/l at six of the nine monitoring stations, including Silver Bow Creek at Opportunity (81.4 µg/l), and the Clark Fork River sites below Warm Springs Creek (6.6 µg/l), above the Little Blackfoot River (8. µg/l), at Bonita (7.7 µg/l), below Missoula (14.7 µg/l), and at Huson (6. µg/l). The lowest median SRP concentration was found in the Clark Fork River above the Flathead River confluence (2.7 µg/l) Summer Summary Statistics Mean, median, minimum, maximum, standard deviation and variance values for 3 for each of the nutrient constituents were calculated for the nine summer nutrient target stations (Appendix E). The Tri-State Water Quality Council s stated objective is to achieve a percent compliance rate at the percent confidence level for each of the summer target values. At a percent confidence level, the allowable number of exceedances for samples is 14.3 percent, or no more than 1 exceedance per samples. In summer 3, compliance with the established total nitrogen target level was met only in the Clark Fork River above Missoula. The total phosphorus target was met only at the Clark Fork River sites at Huson and above the Flathead River. The secondary target for total soluble inorganic nitrogen was met at Clark Fork River sites located at Bonita and above Missoula. The secondary target for soluble reactive phosphorus was not attained at any of the nine monitoring stations. The number of samples exceeding the nutrient target levels during the ten sampling events and the associated percent compliance for each nutrient variable is shown by monitoring station in Table 2-1. Table 2-1. Summer Sample Nutrient Target Compliance Station # above target TN TP TSIN SRP % compliance # above target % compliance # above target % compliance # above target/ % compliance SBC at Opportunity CFR bl Warm Springs CFR at Deer Lodge CFR ab Ltl Blackfoot CFR at Bonita CFR ab Missoula CFR bl Missoula CFR at Huson CFR ab Flathead PERIPHYTON STATISTICS Seven Clark Fork River stations and five Pend Oreille Lake stations have been monitored for periphyton standing crops from 18-3 (Appendix A, Figure ). Clark Fork River stations 11

15 were sampled in August and September. Pend Oreille Lake stations were sampled in September only. Ten replicate samples were collected at each station and these were analyzed for two variables: Chlorophyll a (Chl a) (mg/m 2 ) Ash-free Dry Weight (AFDW) (g/m 2 ) In addition, Secchi disk depth (m) was measured in Pend Oreille Lake as a component of the periphyton monitoring program. 3.1 Temporal Comparison Temporal boxplots for chlorophyll a and ash-free dry weight in periphyton samples from the Clark Fork River (Appendix F) and Pend Oreille Lake (Appendix G) were developed to show changes over the six-year monitoring period Clark Fork River Mean chlorophyll a values for algae samples collected from natural substrates at sites in the Clark Fork River upstream of Missoula had lower mean chlorophyll a values in 3 than in 2. These sites included the Clark Fork at Deer Lodge (7.2 mg/m 2 ), above the Little Blackfoot River (83.8 mg/m 2 ), at Bonita (14.81 mg/m 2 ), and above Missoula (2.32 mg/m 2 ). In 3, the Deer Lodge site had the lowest mean chlorophyll a value recorded in six years of monitoring (18-3). Mean chlorophyll a values in 3 were higher than in 2 at the three Clark Fork River monitoring stations located downstream of Missoula. These included the Clark Fork River below Missoula (16.17 mg/m 2 ), at Huson (.61 mg/m 2 ), and above the Flathead River (17.31 mg/m 2 ). Even though these sites showed mean chlorophyll a values that were greater than those seen in 2, the mean concentrations were still relatively low compared to mean values seen over the entire period of record (18-3). Mean algal biomass values, measured as ash-free dry weight (AFDW), decreased from 2 to 3 at six of the seven monitoring stations. Only the Clark Fork River site above Missoula showed values in 3 that were greater than in 2. In 3 the Clark Fork River sites below Missoula and above the Flathead River exhibited the lowest mean AFDW values recorded in six years of monitoring Pend Oreille Lake Mean chlorophyll a values for algae samples collected from natural substrates in Pend Oreille Lake were higher in 3 than in any previous year of sampling (18-2) when data for all sample sites were pooled. However, the mean values for 3 were quite comparable to previous years when looking at the individual stations data. Mean chlorophyll a increased from 2 to 3 at Bayview (11.27 mg/m 2 ) and Trestle Creek (. mg/m 2 ), but decreased at Kootenai (8.7 mg/m 2 ), Springy Point (12.84 mg/m 2 ), and Sunnyside (7.11 mg/m 2 ). 12

16 Temporal patterns for attached algae measured as mean ash-free dry weight concentrations were similar to those for chlorophyll a. The mean AFDW in 3 for all Pend Oreille Lake stations pooled was the second highest on record, and only behind the 1 sampling year. Mean concentrations increased from 2 to 3 at Bayview (13.33 g/m 2 ), Springy Point (11.31 g/m 2 ), and Trestle Creek(6.76 g/m 2 ), but decreased at Kootenai (8.84 g/m 2 ) and Sunnyside (8.3 g/m 2 ). 3.2 Spatial Comparison Periphyton data for the Clark Fork River (Appendix F) and Pend Oreille Lake (Appendix G) are depicted as spatial boxplots for years Clark Fork River chlorophyll a boxplots include horizontal lines that show the benthic algae chlorophyll a targets levels for both a summer mean ( mg/m 2 ) and annual maximum (1 mg/m 2 ) instream concentration. These targets were developed by the Tri-State Water Quality Council and subsequently adopted as sitespecific water quality standards by the State of Montana (ARM ) Clark Fork River In August 3, five of seven Clark Fork River monitoring locations had mean chlorophyll a values below the mean target level of mg/m 2. These included sites at Deer Lodge (6.6 mg/m 2 ), above the Little Blackfoot River (64.8 mg/m 2 ), above Missoula (4.7 mg/m 2 ), at Huson (44.3 mg/m 2 ), and above the Flathead River (21.4 mg/m 2 ). In September 3, three of seven monitoring sites produced mean chlorophyll a values less than the mean target level, including the Clark Fork above Missoula (.3 mg/m 2 ), at Huson (7.2 mg/m 2 ), and above the Flathead River (13. mg/m 2 ). Additionally, five of the seven sites showed higher mean chlorophyll a values in September than in August, indicating that peak algae growth for 3 likely occurred in the month of September. Two stations, the Clark Fork at Bonita and below Missoula, exceeded the instream summer mean target level in August 3, while the same target level was exceeded instream at four locations during September 3. These four sites included the Clark Fork at Deer Lodge, above the Little Blackfoot River, at Bonita, and below Missoula. If the measured 3 chlorophyll levels for the Clark Fork River are averaged for the August and September sampling events to reflect a summer mean concentration, and these averages are compared to the summer mean state water quality standard for the Clark Fork River, 3 of 7 sites failed to attain the state standard for chlorophyll a in 3 ( mg/m 2 ). These monitoring locations are the Clark Fork at Deer Lodge, Bonita, and below Missoula. Additionally, the individual sample replicate data for chlorophyll a in the Clark Fork River during 3 showed that at least one measurement value for either August or September 3 surpassed the target for maximum growth (1 mg/m 2 ) at six of the seven sites. The only station with all samples below the target maximum (1 mg/m 2 ) in 3 was the Clark Fork River at Huson. Comparisons of the 18-3 algal standing crop data to the relevant target values/water quality standards for the Clark Fork River are shown in Figures 3-1 to 3-7. Mean values are displayed as points on the chart. The target mean ( mg/m 2 ) and maximum (1 mg/m 2 ) chlorophyll a values are displayed as dashed lines. 13

17 3.2.2 Pend Oreille Lake In 3, mean chlorophyll a values from algae samples collected from natural substrates in Pend Oreille Lake were lowest at the Sunnyside site (7.1 mg/m 2 ), and highest at the Springy Point site (12.8 mg/m 2 ) located near the outlet of Pend Oreille Lake. The Trestle Creek site had the lowest mean ash-free dry weight in 3 (6.8 g/m 2 ), while Bayview had the highest mean (13.3 g/m 2 ). For the entire period of record (18-3), the Sunnyside site had the highest mean chlorophyll a (12.8 mg/m 2 ) and AFDW (14.4 g/m 2 ) values. The lowest mean chlorophyll a and AFDW for the entire period of record was attributed to the Bayview site (6.2 mg/m 2 and 7.8 g/m 2, respectively) Mean Chlorophyll A concentration (mg/m2) Aug 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total Figure 3-1. Clark Fork at Deer Lodge chlorophyll a values compared to instream target levels, Mean Chlorophyll A concentration (mg/m2) Aug 18 Sept 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total Figure 3-2. Clark Fork above Little Blackfoot chlorophyll a values compared to instream target levels,

18 3 Mean Chlorophyll A concentration (mg/m2) Aug 18 Sept 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total Figure 3-3. Clark Fork at Bonita chlorophyll a values compared to instream target levels, Mean Chlorophyll A concentration (mg/m2) Aug 18 Sept 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total Figure 3-4. Clark Fork above Missoula chlorophyll a values compared to instream target levels, Mean Chlorophyll A concentration (mg/m2) Aug 18 Sept 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total Figure 3-. Clark Fork below Missoula chlorophyll a values compared to instream target levels,

19 Mean Chlorophyll A concentration (mg/m2) Aug 18 Sept 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total Figure 3-6. Clark Fork at Huson chlorophyll a values compared to instream target levels, Mean Chlorophyll A concentration (mg/m2) Aug 18 Sept 18 Aug 1 Sept 1 Aug Sept Aug 1 Sept 1 Aug 2 Sept 2 Aug 3 Sept 3 Total 1. Figure 3-7. Clark Fork above Flathead chlorophyll a values compared to instream target levels, Secchi Depth Secchi transparency measurements have been collected on Pend Oreille Lake periodically since the 1s. The Bayview, Hope and Granite stations have over years of historical data, and are currently the only stations monitored under the Tri-State Council program (Appendix A, Figure ). Boxplots (Appendix H) show fluctuations in median Secchi depth throughout the period of record. When data for the three current monitoring sites are pooled, the highest median value (or highest water transparency) was documented in 3, with the lowest median value found in 1. Secchi depth readings were typically highest in winter, with lowest values recorded in spring. The Bayview station experienced the greatest median Secchi depth readings, while the Hope site had the lowest median Secchi depth readings for the period of record. Secchi disk depth measurements were collected nine times in 3 at the Granite site, and three times in 3 at Hope and Bayview. Of these three sites, Bayview had the highest median 16

20 Secchi transparency (16.2 meters), followed by Granite (12. m) and Hope (11. m). The lowest Secchi depths recorded in 3 were experienced in spring, with the greatest depths occurring in winter. Additionally, the individual median Secchi disk readings for all three sites during 3 were the highest on record. 17

21 4. REFERENCES Administrative Rules of Montana. 2. Numeric Algal Biomass and Nutrient Standards for the Clark Fork River. ARM , Effective August 16, 2. Idaho Fish & Game. 3. Pend Oreille Lake Fishery Recovery Project Annual Progress Report for 2 (draft). Coeur d Alene, ID. Land & Water Consulting, Inc. 1. Water quality status and trends monitoring system for the Clark Fork-Pend Oreille Watershed. Prepared for the Tri-State Implementation Council. Missoula, MT. Land & Water Consulting, Inc. 3a. Water Quality Status and Trends Monitoring System for the Clark Fork-Pend Oreille Watershed Summary Monitoring Report 2. Prepared for Tri-State Water Quality Council. Missoula, MT. Land & Water Consulting, Inc. 3b. Clark Fork-Pend Oreille Watershed Water Quality Monitoring Program - Quality Assurance Project Plan. Prepared for Tri-State Water Quality Council. Missoula, MT. Tri-State Implementation Council (now the Tri-State Water Quality Council). 18. Clark Fork River Voluntary Nutrient Reduction Program, August 18. Sandpoint, Idaho. U.S. Environmental Protection Agency. 13. Clark Fork-Pend Oreille Basin Water Quality Study A Summary of Findings and a Management Plan. Conducted under Section 2 of the Clean Water Act of 187. U.S. Environmental Protection Agency, Regions 8 and, State of Montana, State of Idaho, State of Washington. January 13. Seattle, WA. Walker, W.W. 1. Simplified Procedures for Eutrophication Assessment and Prediction: User Manual. Instruction Report W-6-2, US Army Corps of Engineers Waterways Experiment Station, updated April 1. 18

22 Appendix A WATER QUALITY MONITORING STATIONS AND SAMPLING FREQUENCY/FIGURES TABLE 1 WATER QUALITY MONITORING STATIONS AND SAMPLING FREQUENCY, 3 FIGURE 1 PROJECT STUDY AREA FIGURE 2 WATERSHED BOUNDARIES FIGURE 3 NUTRIENTS AND METALS CONCENTRATIONS MONITORING SITES FIGURE 4 ADDITIONAL SUMMER NUTRIENT MONITORING SITES FIGURE PERIPHYTON DENSITY MONITORING SITES Clark Fork-Pend Oreille Watershed Summary Monitoring Report

23 Appendix A, Table 1 Water Quality Monitoring Stations and Sampling Frequency, 3 Station Name Sampling Frequency 2. Silver Bow Creek at Opportunity S 7 Clark Fork below Warm Springs Creek S Clark Fork at Deer Lodge P, S Clark Fork above Little Blackfoot River P, S 12 Clark Fork at Bonita P, S 1. Clark Fork above Missoula P, S 18 Clark Fork below Missoula (Shuffields) P, S 22 Clark Fork at Huson P, S 2 Clark Fork above Flathead P, S 27. Thompson River near mouth N12 28* Clark Fork below Thompson Falls NM12 2* Clark Fork at Noxon Bridge NM12 3* Clark Fork below Cabinet Gorge Dam NM18 Pend Oreille River at Newport, WA Pend Oreille River at Metaline Falls, WA Pend Oreille Lake: Kootenai Pend Oreille Lake: Springy Point Pend Oreille Lake: Sunnyside Pend Oreille Lake: Trestle Creek Pend Oreille Lake: Bayview Pend Oreille Lake: Hope Pend Oreille Lake: Granite Point N12 N12 P P P P P, SD SD SD N12 = Nutrient and field constituents, 12 monthly samples NM12 = Nutrient, metal and field constituents, 12 monthly samples NM18 = Nutrient, metal and field constituents, 12 monthly samples and 6 peak flow samples P = Periphyton, replicates per site, August and September (September only on Pend Oreille Lake) S = Summer nutrient and field constituents, samples during 3 weeks in summer SD = Secchi Depth, 12 monthly samples (if available) * These sites sponsored by Avista Corp., pursuant to 41 certification requirement

24 # ék P e n d O r e i l l e R i v e r Metaline Falls Box Canyon Dam Priest Lake Kalispel Tribe # Newport Sandpoint # Lake Pend Oreille Albeni Falls Dam Cabinet Gorge Dam # Noxon C Noxon Falls Dam l a r k Thompson Falls Dam Thompson Falls # F o r k R i v e r # St. Regis Kalispell # Flathead Lake F l a t h e a d R i v e r Flathead Indian Reservation Washington British Columbia, Canada Idaho Montana R i v e r B i t t e r r o o t Milltown Dam # Missoula B C l a l a c k f o o t r k F o r k R i v e r R i v e r # Deer Lodge Butte# Figure 1. Project Study Area Clark Fork - Pend Oreille Basin N W E S 2 2 Miles Project#: 328 Date: June 3 Location: Clark Fork-Pend Oreille Basin Project Manager: G. Ingman Drawn By: M. Arthur LAND & WATER CONSULTING, INC. 11 Cedar Street PO Box 824 Missoula, MT 87

25 # Metaline Falls PEND ORIELLE WA ID PRIEST NORTH FORK FLATHEAD # Newport Sandpoint # LAKE PEND OREILLE ID MT # Noxon LOWER CLARK FORK Thompson # Falls STILLWATER Kalispell # FLATHEAD LAKE MIDDLE FORK FLATHEAD SWAN SOUTH FORK FLATHEAD # St. Regis LOWER FLATHEAD British Columbia, Canada MIDDLE CLARK FORK Missoula # BLACKFOOT Washington Montana Idaho BITTERROOT FLINT-ROCK # Deer Lodge UPPER CLARK FORK Butte# Figure 2. Watershed Boundaries Clark Fork - Pend Oreille Basin N W E S 2 2 Miles Project#: 328 Date: June 3 Location: Clark Fork-Pend Oreille Basin Project Manager: G. Ingman Drawn By: M. Arthur LAND & WATER CONSULTING, INC. 11 Cedar Street PO Box 824 Missoula, MT 87

26 Figure 3. Nutrient and Metal Concentration Monitoring Sites Clark Fork - Pend Oreille Basin e POR/METALINE % WA ID P e n d O r e i l l e R i v e r Priest Lake POR/NEWPORT % Lake Pend Oreille $ ID MT CFK/Cabinet Gorge D # CFK / Noxon B Flathead Lake CFK bl Thompson Falls C # l a r k % F o r k Thompson R R i v e r a d R i v e r F l a t h Monitoring Site % Sampling Frequency = 12, Nutrients Only # Sampling Frequency = 12, Nutrients and Metals $ Sampling Frequency = 18, Nutrients and Metals R i v e r B l a c f k C l a r o o t R i v e r k F o r k R i v e r B i t t e r r o o t Project#: 328 Date: June 3 Location: Clark Fork-Pend Oreille Basin Project Manager: G. Ingman Drawn By: M. Arthur N W E S 2 2 Miles LAND & WATER CONSULTING, INC. 11 Cedar Street PO Box 824 Missoula, MT 87

27 Figure 4. Additional Summer Nutrient Monitoring Sites Clark Fork - Pend Oreille Basin P e n d O r e i l l e R i v e r WA ID Priest Lake Lake Pend Oreille ID MT Flathead Lake C l a r k F o r k R i v e r # CFK/Flathead F l a t h e a d R i v e r Monitoring Site (Extra Summer Sample) # Sampling Frequency = # CFK/Shuffields CFK/Huson R i v e r B i t t e r r o o t ## B l a c k CFK/Missoula CFK/Bonita# o t f o C la r k R i v e r F o r k R i v CFK/Little Blackfoot R CFK/Deerlodge CFK/Warm Sp Cr Silver Bow/Opportunity e r # # # # Project#: 328 Date: June 3 Location: Clark Fork-Pend Oreille Basin Project Manager: G. Ingman Drawn By: M. Arthur N W E S 2 2 Miles LAND & WATER CONSULTING, INC. 11 Cedar Street PO Box 824 Missoula, MT 87

28 Figure. Periphyton Density Monitoring Sites Clark Fork - Pend Oreille Basin P e n d O r e i l l e R i v e r Kootenai Sunnyside %U %U %U%U Trestle Springy "Á Hope Point "Á Granite Point %U"Á Bayview ID MT WA ID Priest Lake Lake Pend Oreille Flathead Lake C l a r k F o r k R CFK/Flathead i v e r # h e a d F l a t R i v e r Sandpoint %U # %U %U Trestle %U Sunnyside "Á Springy Hope Point Lake Pend Oreille "Á Granite Point %U "Á Bayview Miles # CFK/Shuffields CFK/Huson R i v e r B i t t e r r o o t ## B CFK/ Missoula CFK/Bonita l a c k f # C o o t la r k R i v e r F o r k CFK/Little Blackfoot R R i v e r CFK/Deer Lodge # # Monitoring Site "Á Secchi Disk # River Sites %U Lake Sites Project#: 328 Date: June 3 Location: Clark Fork-Pend Oreille Basin Project Manager: G. Ingman Drawn By: M. Arthur N W E S 2 2 Miles LAND & WATER CONSULTING, INC. 11 Cedar Street PO Box 824 Missoula, MT 87

29 Appendix B 3 WATER QUALITY DATA SPATIAL BOXPLOTS Clark Fork-Pend Oreille Watershed Summary Monitoring Report

30 ..4.3 Total Nitrogen (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall.3 Total Soluble Inorganic Nitrogen (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall Non-detectable concentrations reported as ½ detection limit. Not all extreme values shown on boxplots.

31 .4.3 Total Phosphorus (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall..8 Soluble Reactive Phosphorus (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall Non-detectable concentrations reported as ½ detection limit. Not all extreme values shown on boxplots.

32 ..4 Total Kjeldahl Nitrogen (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall Nitrate + Nitrite (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall Non-detectable concentrations reported as ½ detection limit. Not all extreme values shown on boxplots.

33 Ammonium (mg/l) Thompson River CFR at Noxon POR at New port CFR bl Thompson Fall CFR bl Cabinet Gorge POR at Metaline Fall.4 Total Recoverable Copper (mg/l) Thompson River CFR at Noxon CFR bl Thompson Fall CFR bl Cabinet Gorge Non-detectable concentrations reported as ½ detection limit. Not all extreme values shown on boxplots.