Decision Support Tool for Water Management and Environmental Flows: Mill Creek Case Study. JENNY TA B.S. (Massachusetts Institute of Technology) 2004

Transcription

1 Decision Support Tool for Water Management and Environmental Flows: Mill Creek Case Study By JENNY TA B.S. (Massachusetts Institute of Technology) 2004 THESIS Submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in Hydrologic Sciences in the OFFICE OF GRADUATE STUDIES of the UNIVERSITY OF CALIFORNIA DAVIS Approved: Joshua H. Viers, Chair Jay R. Lund Samuel Sandoval-Solis Committee in Charge 2015 i

2 Table of Contents List of Figures... iii List of Tables... v Acknowledgements... vi Abstract... 1 Introduction... 3 Mill Creek Case Study Methods Results Discussion Conclusion References ii

3 List of Figures Figure 1. Map of Mill Creek watershed in Tehama County, California (elevation contour in meters) Figure 2. Map of lower reach of Mill Creek by the town of Los Molinos Figure 3. Annual flows for water years for upstream (MLM) and downstream (MCH) stream gauges on lower Mill Creek Figure 4. Difference in annual water volume between upstream and downstream gauges in lower Mill Creek for water years with Sacramento Valley Index water year types indicated (C = critically dry, D = dry, BN = below normal, AN = above normal, W = wet) Figure 5. Flow exceedance probabilities for upstream (MLM) and downstream (MCH) gauges for water years Figure 6. Model schematic Figure 7. Three environmental flow cases: a seasonal fall and spring fish passage flow, a 2.55 cms minimum instream flow, and an 80% sustainability boundary flow Figure 8. Modeled and observed lower Mill Creek outflow for water year 2008 with baseline water management (NSE = 0.92) Figure 9. Fish passage environmental flow allocations and total water diversions for water year 2008 with baseline water management Figure 10. Fish passage environmental flow shortages for critically dry water year 2008 with baseline water management Figure 11. Fish passage shortages for critically dry (2008), below normal (2010), and wet (2006) water year types for five water management alternatives: baseline, 4 wells, water agreement, water agreement and 4 wells, and leaving Droz and Orange Cove instream. The x-axis corresponds to water year weeks and the y-axis correspond to water volume shortages in mcm Figure 12. Percent change of fish passage flow shortages for different water management alternatives compared to baseline for critically dry water year Figure 13. Percent change of fish passage flow shortages for different water management alternatives compared to baseline for below normal water year Figure 14. Percent change of fish passage flow shortages for different water management alternatives compared to baseline for wet water year iii

4 Figure 15. Minimum instream flow shortages for critically dry (2008), below normal (2010), and wet (2006) water years for baseline, 4 wells, water exchange agreement, agreement and 4 wells, Droz and Orange Cove left instream, and LMMWC water left instream. The x-axis corresponds to water year weeks and the y-axis corresponds to water volume shortages in mcm Figure 16. Percent change of minimum instream flow shortages for different water management alternatives compared to baseline for critically dry water year Figure 17. SBA environmental shortages for critically dry (2008), below normal (2010), and wet (2006) water years for baseline, 4 wells, agreement, agreement and 4 wells, Droz and Orange Cove purchase, and LMMWC purchase management options. The x-axis is in water year weeks and the y-axis is water volume shortages in mcm iv

5 List of Tables Table 1. Model inputs, example variable values, data types, and sources Table 2. Description of different water management options used in model runs Table 3. Annual volume of shortages for fish passage, MIF, and SBA environmental flow cases by water year type and water management alternatives. Percent decrease in environmental flow shortage from baseline indicated in parentheses v

6 Acknowledgements I would like to acknowledge the financial support for this research from the UC Davis Center for Watershed Sciences, The Nature Conservancy, and the UC Davis Hydrologic Sciences Graduate Group Fellowship. Rodd Kelsey, Gregg Werner, and Jeanette Howard of The Nature Conservancy provided valuable insight on the Mill Creek watershed essential to developing a representative model. Countless members of the Shed provided valuable feedback and discussion, in particular members of Professor Jay Lund s Water Systems Research group. Special thanks are extended to my advisor Josh Viers and committee members Jay Lund and Sam Sandoval for their invaluable encouragement and support. Finally, thanks to my family and Albert for everything. vi

7 Jenny Ta June 2015 Hydrologic Sciences Abstract Stream flow drives many physical and ecological processes in rivers that support freshwater ecosystems. Human activities like dam operations, water diversions, and flood control infrastructure together have fundamentally altered many streams. Water scarcity from increasing water demands and prolonged droughts has further stressed freshwater ecosystems, which in turn is prompting the development of new methods and tools for establishing environmental flows. This study developed a linear programming model for exploring the effects of water management alternatives on environmental flows in river systems that have minimal or no regulation from dam operations, but still have altered flow regimes due to surface water diversions. The model was applied to a case study on Mill Creek, a tributary of the Sacramento River in northern California s Tehama County, whose altered flow regime affects fall and spring fish migration to upstream spawning habitat. Test cases were used to examine how water management alternatives can improve environmental flow allocations while striving to meet agricultural water supply demands. These test cases included: 1) fish passage flows for California Central Valley Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss); 2) a 2.55 cms minimum instream flow (MIF); and 3) a sustainability boundary approach (SBA) with a flow target of 80% of natural flow. The model quantifies the effect of water management alternatives such as conjunctive use, water rights transfers, and water exchange agreements on instream environmental flow conditions. The model identified the 1

8 last two weeks of October as a consistent period of shortage for fall fish passage flows during all water year types from critically dry to wet water years. Shortages to fish passage flows could be eliminated through the combined use of a water exchange agreement and conjunctive use wells. The MIF and SBA environmental flow cases both required acquisition of the largest water right holder in the system to decrease environmental shortages by over 80%. This modeling approach can be applied to other river systems as a decision-support tool for conservation organizations and government agencies to make more informed decisions regarding management of scarce water resources to maximize ecological function while minimizing impact on human uses of water. 2

9 Introduction Rivers carry only percent of water globally (Shiklomanov 1993), but support 6 percent of biodiversity that has been discovered (Dudgeon, Arthington et al. 2006). However, flows in rivers have been transformed due to their usefulness to society. Dams built to harness the power of a river interrupt its flow and sever its tie to natural rainfall and runoff, allowing humans to dictate river flow. Water diversions siphon volumes of water from rivers to supply water, sometimes leaving rivers trickling or dry. Human activities like dam operations, water diversions, and flood control infrastructure have impacts beyond biodiversity, as rivers provide critical ecosystem services that human societies depend on (Dudgeon 2010, Arthington 2012). For example, the rich diversity of species in freshwater ecosystems supports economic productivity such as fisheries. They are also a valuable source of genetic information and promote cleaning of water (Dudgeon, Arthington et al. 2006). Biologically complex and functionally intact freshwater ecosystems provide goods and services like food supply, purification of industrial and human wastes, flood control, and plant and animal habitats and also contribute to adaptive capacity to future environmental alterations like climate change (Baron, Poff et al. 2002). Since biodiversity declines are greater in freshwater ecosystems than in most terrestrial ecosystems, it can be said that freshwater ecosystems are the most endangered ecosystems in the world (Sala, Chapin III et al. 2000). For these reasons, there is an urgent need for sustainable water resource allocation to maintain the processes that support freshwater ecosystem integrity. 3

10 Natural Flow Regime Paradigm The ecological integrity of riverine ecosystems depends on the natural dynamic character of streamflow captured by five components of flow regime: magnitude, frequency, duration, timing, and rates of change. Thus, streamflow has been identified as a master variable that controls physical and ecological processes in rivers (Poff, Allan et al. 1997), and its regulation is increasingly important for environmental management. For instance, high magnitude flows create disturbance through scour and provide sediments which initiate succession in riparian forests (Rood, Samuelson et al. 2005). In addition, reproductive success of riparian and riverine species such as cottonwood (Populus spp.) and the foothill yellow-legged frog (Rana boylii) depend on the timing and rate of change of the spring snowmelt recession of Mediterranean-montane streams (Yarnell, Viers et al. 2010). However, modifications of a river s natural flow regime such as from the construction of dams for hydroelectric power and water supply have negatively impacted aquatic species that have evolved to depend on a river s natural flow. Altered flow regimes have been shown to affect aquatic biodiversity in streams and rivers (Bunn and Arthington 2002) and have also been linked to changes in human well-being (Naiman and Dudgeon 2011). Even small spatially distributed reservoirs affect river flow (Deitch, A.M. et al. 2013). Accelerating degradation of freshwater ecosystems (Dudgeon, Arthington et al. 2006) due to human water use threaten both human water security and river biodiversity (Vorosmarty, McIntyre et al. 2010). For freshwater conservation to be viable for the long-term, water management must make compromises between human livelihoods, biodiversity conservation, and ecosystem function. Thus, there is growing recognition of the need to conserve freshwater 4

11 ecosystems and biodiversity through identifying and allocating environmental flows. Environmental Flow Science Environmental flows characterize the quantity, timing, and quality of water in rivers required to sustain freshwater or estuarine ecosystems and the human well-being that relies on these ecosystems (Brisbane Declaration 2007). Several approaches to developing environmental flow requirements exist from the most basic minimum instream flows, to statistical Tennant Methods, ELOHA, percent change from natural flow (SBA), and hydraulic modeling approaches (Tharme 2003). One approach to environmental flows is to limit the extent of alteration to a natural flow regime or to design flow regimes for specific ecological functions in regulated rivers (Acreman, Arthington et al. 2014). While some studies focus on water abstraction restrictions (Acreman, Dunbar et al. 2008) and the effect of small-scale spatially distributed water reservoirs (Deitch, A.M. et al. 2013), most environmental flow studies focus on reservoir re-operation of large centralized water management systems (Richter and Thomas 2007, Yin, Yang et al. 2011, Shiau and Wu 2013, Jager 2014). An example of reservoir re-operation for environmental flows was the implementation of dam operation requirements on Putah Creek to restore specific flow requirements to support native fish (Kiernan, Moyle et al. 2012). Kiernan et al found that following implementation of a design flow that mimicked natural early spring pulse flows increased the proportion of native fish species in reaches previously dominated by alien fish species. 5

12 Though there has been a lack of studies and development of tools to facilitate allocation of environmental flows in diversion-impacted rivers, a landmark 1983 California Supreme Court case set precedent for preserving natural environmental capital by invoking the public-trust doctrine (Dunning 1989). In this case, the City of Los Angeles Department of Water and Power was obligated to protect Mono Lake s ecosystem by reducing water supply diversions to preserve environmental flows (Koehler 1995). Growing water demands and global climate change has exacerbated the uncertainty of water availability and conflict among water users. From 2012 to the time of publication of this paper, California is experiencing a major drought (Swain, Tsiang et al. 2014), forcing difficult decisions regarding the allocation of water, such as mandatory reduction of diversions from rivers to provide minimum flows for state and federally-listed anadromous fish (CA State Water Resources Control Board 2015). An uncertain and scarce water supply coupled with competing water demands calls for tools that enable people to make better management decisions. This research addresses water scarcity in diversion-impacted rivers using a decision-support tool to explore water management alternatives to meet agricultural water supply needs while striving for maximum support of freshwater ecosystems. 6

13 The model developed in this study explored the following research questions: 1. Given a specific environmental flow target, represented as a design hydrograph in a river subject to water abstractions, when and to what extent is there insufficient water to meet environmental flow demands? 2. What are the effects of different water management alternatives on instream environmental flow? 3. How do water management alternatives perform in different water year types? Water transfers are an emerging management tool for acquiring water to support freshwater ecosystems. To make informed decisions on financial investments in water transfers for the environment, it is necessary to understand when water transfers would be needed and the volume needing to be transferred. The first question explored in this study aims to quantify when and by how much environmental flow targets are not met. A combination of water management alternatives may be needed to acquire enough water for environmental flow. For this reason, it is useful for decision makers to understand how different water management options will reduce environmental flow shortages. In addition, water management alternatives for meeting environmental flow targets may change between wet and dry years. For this reason, this study also explores the effect of different water management alternatives during different water year types as defined by the Sacramento Valley Index (DWR 2013). 7

14 Central Valley Chinook Salmon and Steelhead Trout Life history requirements for Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) were used as test cases to explore how different water management alternatives can improve environmental flow objectives while minimizing impact to local agricultural water supply, as environmental flow requirements aimed at protecting broad-based ecological function are increasingly being used to manage these freshwater species as both are threatened species (Central Valley spring-run Chinook salmon are listed as threatened in the state and federal Endangered Species Acts and the California Central Valley steelhead trout are listed a threatened in the federal Endangered Species Act (CA Department of Fish and Wildlife 2015)). Pacific salmon have important cultural, ecological, and economic value throughout their range. Ecologically, salmon are a keystone species, transporting productivity from the ocean into terrestrial systems (Gende, Edwards et al. 2002). Nutrients brought inland by salmon are found in terrestrial food chains in species from eagles to riparian vegetation (Cederholm, Kunze et al. 1999). They are born and reared in freshwater streams, then migrate to the ocean to mature, and finally returning to their native freshwater stream years later to spawn. While most salmon migrate relatively short distances to spawn (less than 150 km), some can migrate more than 2,000 km to spawning habitat, such as in the Yukon River in Alaska (Moyle 2002). These focal species, like all anadromous Pacific salmon, have been harmed by myriad effects of global environmental change, including direct human effects on river ecosystems. 8

15 Salmon migrate approximately 450 km from the San Francisco Bay, up the Sacramento River to spawning habitat on Mill Creek (Tehama County, CA), one of the highest known spawning elevation for Pacific salmon at 1,800 meters (Moyle 2002). Mill Creek contains spawning habitat for spring and fall-run Chinook salmon and steelhead trout. Spring and fall-run species are two of four major Central Valley runs (fall, late-fall, winter, spring) of distinct populations within the species that exhibit genetically-based adaptations to regional environments. Central Valley Chinook salmon are categorized into two basic life history types: ocean-type and stream-type. The juveniles of ocean-type fish spend a short amount of time (3-12 months) rearing in freshwater and spawn soon after entering freshwater as adults returning from the ocean. In contrast, stream-type juvenile fish spend over a year rearing in freshwater and return to freshwater streams from the ocean before reaching full maturity (Moyle 2002). The Central Valley spring-run evolutionary significant unit (ESU) includes populations in the Sacramento and San Joaquin River, though the San Joaquin spring-run has become extinct (Moyle 2002). While spring-run Chinook salmon (SRCS) were once the most abundant in the Central Valley, populations have declined to the point where only remnant populations remain in Butte, Mill, Deer, and Antelope Creeks (DFW, 1998). These remaining headwater habitats were historically minor habitats for the once abundant SRCS (Moyle 2002), whose spawning grounds were blocked by the construction of dams on many Sacramento tributaries. 9

16 SRCS have a classic stream-type life history pattern. They enter the Sacramento River as immature fish from late-march through September, migrate as far upstream as possible, then hold over in deep, cold-water pools over the summer. Spawning occurs in early fall (mid-august through early-october). Juveniles emerge in November through March, rearing in streams from 3 to 15 months. Outmigration of juvenile salmon occurs during all months in the Sacramento River in various sizes (from fry to smolts), with peak outmigrations occurring in winter (Jan-Feb) and then again in spring (April) (Moyle 2002). Mill Creek, the case study developed in this research, is seasonally dewatered in the summer low flow season, impairing this seasonal fish migration. 10

17 Mill Creek Case Study Mill Creek, in Tehama County, California, runs approximately 95 kilometers from the peak of Mount Lassen to the Sacramento River, draining 342 km 2 of watershed (Figure 1). Due in part to its rugged terrain, the higher elevation reaches (> 1000 m) of this river have remained largely undisturbed by human development and still support holding and spawning habitat for spring-run Chinook salmon and steelhead (Palmer 2012). In the lower gradient reach flows, prior to flowing through the unincorporated town of Los Molinos and reaching its confluence with the Sacramento River, Mill Creek is subject to several water diversions. The irrigation season is April 1 st to October 31 st, during which water is withdrawn from the lower reaches of Mill Creek at two diversions for agricultural users in the Los Molinos area to irrigate orchards and pastureland. Two stream gauges are in the lower Mill Creek reach (Figure 2), an upstream gauge (USGS , hereafter referred to with CDEC code MLM standing for Mill at Los Molinos) and a downstream gauge (DWR A004420, hereafter referred to with CDEC code MCH for Mill Creek at Highway 99). Two diversions, the Upper Diversion Dam and Warn Dam, are operated by the Los Molinos Mutual Water Company with a combined diversion capacity of 150 cfs (G. Werner, personal communication, January 17, 2015). Since the watershed is fully allocated, diversions from these two points during the irrigation season have can dewater the lower reaches of Mill Creek during summer low flows. In an effort to restore summer in-stream flows, an Interagency Water Exchange Agreement has been created to exchange groundwater pumping for irrigation in return for decreases in surface water diversions during fish migration seasons (Heiman and Knecht 2010). 11

18 Figure 1. Map of Mill Creek watershed in Tehama County, California (elevation contour in meters). Water rights on Mill Creek were fully adjudicated by the state in the 1920s (Superior Court of Tehama County 1920). Flows up to 5.7 cms (203 cfs) are allocated to water users, which covers most, if not all, summer base flow in Mill Creek. Since the entire river flow is allocated from 5.7 cms (203 cfs) and below, diversions during the low flow season lead to dewatering of the river downstream of Ward Dam, impairing migration of spring and fall-run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss). 12

19 Mill Creek Watershed Sacramento River Upper Diversion Dam Mill Creek! Ward Dam! MLM gauge!(!( MCH gauge Figure 2. Map of lower reach of Mill Creek by the town of Los Molinos Kilometers During the irrigation season from April 1st to October 31st, flows in lower Mill Creek can be dewatered. Figure 3 shows annual flows for both gauges for water years 1999 to There is a 38 to 70 mcm (31,000 to 57,000 acre-feet) annual difference in water volume between the upstream and downstream gauges (Figure 4). 13

20 Figure 3. Annual flows for water years for upstream (MLM) and downstream (MCH) stream gauges on lower Mill Creek. Figure 4. Difference in annual water volume between upstream and downstream gauges in lower Mill Creek for water years with Sacramento Valley Index water year types indicated (C = critically dry, D = dry, BN = below normal, AN = above normal, W = wet). 14

21 Flow exceedance probabilities (Figure 5) were computed with available data for the period of record for the two stream gauges. This period of record is restricted by the downstream MCH stream gauge which only has data available for water years 1999 through The impact of diversions during the irrigation season can be seen in the low exceedance discharges on the downstream gauge. Figure 5. Flow exceedance probabilities for upstream (MLM) and downstream (MCH) gauges for water years

22 Methods A linear programming model of the Mill Creek case study was developed to examine environmental flow cases and simulate water management alternatives. The model represents the lower Mill Creek river reach, which is subject to multiple diversions and an evolving environmental flow requirement. Figure 6 shows a schematic of the Mill Creek environmental flow model with two diversions, A 1,t and A 2,t, each representing individual water users with diversion demands that change with time. Inflow into the reach of interest is represented by I t. I t A 1,t A 2,t A E,t O t Figure 6. Model schematic. Environmental flow allocation, A E,t, is represented as a water user in the system with flow requirements downstream of all diversions. Water diverted from the river is transported through canals to agricultural users, most of which are outside the Mill Creek watershed boundary. For this reason, the model assumes no return flows to Mill Creek from water users. The model also assumes negligible stream accretion. Outflow, calculated from the following water balance, O t, at the downstream end of the river reach, is 16

23 where i is each water diverter in the system, and n is the total number of water diverters in the system. Environmental flow allocations are not included in the water balance equation because they represent water that stays in the river and is a component of outflow. Each water user has a time dependent water demand, represented by D i,t. Environmental flow demand is represented by D E,t, which is determined by a design hydrograph developed for specific environmental flow requirements. All water users, including the environmental user, are assigned a shortage penalty coefficient, p, that reflects water right priority. Decision variables are allocations to all water users, both human and environmental demands. The objective function minimizes the sum of the penalty-weighted shortages, as follows. Minimize: Z = nx P i,t (D i,t A i,t ) + X P E,t (D E,t A E,t ) i Subject to: No negative diversions. Diversions cannot exceed water demand. No negative outflow. Inflow must be greater than or equal to sum of allocations 17

24 The linear programming model was implemented in Microsoft Excel 2010 with the OpenSolver 2.6 add-in 1. The model inputs required are upstream inflow discharge, downstream outflow discharge, water diversion demands in the system, and a desired time-series hydrograph representing the environmental flow target of interest (Table 1). Modeled decisions that can vary to represent different water management options are the irrigation periods for each water right holder, the option to purchase and leave instream individual water rights, and the number, pumping capacity, and use of conjunctive use wells

25 Table 1. Model inputs, example variable values, data types, and sources. Inputs Example Variable Values Data Type Source Inflow stream gauge data time series (csv file) USGS; CDEC (weekly time step) water year types: critically dry string Sacramento dry Valley Index below normal above normal wet Water Rights weekly diversion rate (cfs) numeric float 1920 Tehama (Irrigation Demand) Court Decree Environmental Flow Target seasonal fish passage flows discharge time series 2014 DFW, NMFS minimum instream flows (weekly time step) Drought Agreement percentage of full natural flow functional flows Priority Ranking of Users Shift priority of environmental user integer 1920 Tehama 1 = highest priority Court Decree Water Management Options Irrigation Period April 1 to October 31 boolean user defined shifting periods of diversion 1 = irrigated 0 = not irrigated Groundwater Wells number of wells numeric integer user defined well capacity numeric float Water Exchange Agreements instream environmental flow boolean user defined TNC water rights available for irrigation numeric float Individual Water Rights leave instream or divert boolean user defined Model Validation Water inflow values into lower Mill Creek were taken from USGS ( ) stream gauge readings. A 1920 Tehama County Superior Court decree designated a table that defines water rights for all water users in the system based on the amount of water in Mill Creek from 5.75 cms and below (Superior Court of Tehama County 1920). The model uses these water right values for each water user and assumes that these amounts will be diverted from the river and taken as water demand input for the model. Although not all water users will divert the entire amount of their water right, this conservative approach to modeling diversion amounts much can help 19

26 guarantee flows for instream environmental purposes. These water demands were then used as input in the model to simulate river flow for five representative water year types defined by the Sacramento Valley Water Year Index as defined by the California Department of Water Resources (DWR 2013). Model testing was conducted by comparing simulated outflows with observed discharge at the downstream DWR MCH gauge through the calculation of Nash-Sutcliffe efficiencies (NSE). NSE were computed with the following equation (Moriasi, Arnold et al. 2007): NSE =1 " P n i=1 Y obs P n i=1 i Y sim i 2 Y obs i Y mean 2 # Y obs Y sim where i is the i-th observation of discharge at the DWR MCH gauge, i is the i-th simulated value, Y mean is the mean value of observed discharge, and n is the total number of observations. 20

27 Environmental Flow Targets Figure 7 illustrates three environmental flow cases run in the model: 1. A design hydrograph representing target environmental flow for minimum fish passage flows was created based on minimum flow requirements set during 2014 Volunteer Drought Agreements between the National Marine Fisheries Service and the California Department of Fish and Game and water rights holders on Mill Creek in Tehama County (Howard 2014). Spring base flows of 1.42 cubic meters per second (cms) from April 1 st to June 14 th are required for adult SRCS and juvenile SRCS and steelhead followed by 0.71 cms from June 15 th to June 30 th for juvenile SRCS and steelhead. In the fall, base flows of 1.42 cms are required for out-migrating juvenile SRCS and steelhead and upstream migration of adult steelhead from October 15 th to December 31 st. Pulse flows to attract upstream migration of adult SRCS are needed to mimic the natural increases in stream flow due to spring precipitation and snowmelt. From April 15 th to June 14 th, a minimum pulse flow of 1.42 cms greater than the base flow is required for a minimum of 24 hours once every two weeks. Since the model uses a weekly time step, the 24 pulse flows recommended to cue migration were included in the design hydrograph by calculating the corresponding volume of water needed for each pulse flow and adding that volume to the weekly flow demand. These flow requirements provide the minimum flows needed for migration of adult and juvenile fish in lower Mill Creek below Ward Dam. 2. A second environmental flow case was based on preliminary recommendations from the 21

28 Central Valley Freshwater Needs Assessment conducted by The Nature Conservancy that analyzed stream gauge data from the upstream Mill Creek MLM gauge using the Indicators of Hydrologic Alteration (IHA) software (Richter, Baumgartner et al. 1996). This study indicated that a minimum instream flow of 2.55 cms would be ideal for supporting a suite of freshwater focal species such as cottonwood (Populus sp.), freshwater mussels (Margaritifera falcata), western pond turtle (Actinemys marmorata), bank swallow (Riparia riparia), as well as Chinook salmon and steelhead and resident native fish. 3. A third environmental flow case was based on the concept of a sustainability boundary limit that defines the extent of tolerable hydrologic alteration in the system (Postel and Richter 2003). 80% of full natural flow was chosen as a representation of a sustainability boundary environmental flow target for the purposes of running the model. However, a real-life implementation of the sustainability boundary approach (SBA) require management goals set by water managers in collaboration with local stakeholders. 22

29 Figure 7. Three environmental flow cases: a seasonal fall and spring fish passage flow, a 2.55 cms minimum instream flow, and an 80% sustainability boundary flow. Model Runs Each environmental flow case was run with a selection of water management alternatives (Table 2). One water management option expands the use of pumping groundwater to meet water supply demands thereby allowing more water to be left instream to meet environmental flow requirements. Two wells are currently available with a combined capacity of 0.28 cms. Based on this information, potential new wells were represented with individual capacities of 0.14 cms in the simulation model. Another water management option was to purchase water rights from individual users in the system and leave the water instream to meet environmental flow requirements. Of the eleven water right holders in the system, the Droz and Orange Cove rights have been under consideration for potential water exchange or transfer negotiations and where 23

30 therefore chosen to be simulated in the model as potential water transfers. The Los Molinos Mutual Water Company (LMMWC) rights have the largest percent (68%) of water rights in the system and was selected as a water transfer option in the simulation to quantify its effect on meeting the MIF and SBA cases as these required the largest volume of water. A third management option is a water exchange between The Nature Conservancy (TNC) and LMMWC in which existing TNC water rights would be available for diversion between July 1 st and October 14 th. In return, LMMWC would leave 0.68 cms (24 cfs) instream after October 15 th for approximately three weeks to supplement the TNC instream flows for fall fish passage through lower Mill Creek. Table 2. Description of different water management options used in model runs. Water Management Option Description Baseline Irrigation period for all water users from April 1 to October 31 TNC water rights left instream year round Groundwater Wells Water Exchange Agreement Water Rights Purchase Combination 4 wells each with a pumping capacity of 5 cfs (0.14 cms) TNC water rights diverted from July 1 to October 14, left instream otherwise Supplemental instream flows of 24 cfs for 3 weeks (October 15 to early November) Purchase of water rights to leave instream Droz, Orange Cove, Los Molinos Mutual Water Company (LMMWC) Combined 4 wells and water exchange agreement Each environmental flow case and water management alternative were run with representative water year types based on the California Department of Water Resources Sacramento Valley Index (DWR 2013). The following representative water year types were selected for model runs: critically dry (2008), dry (2009), below normal (2010), above normal (2005), and wet (2006). 24

31 Results The model identified periods of water scarcity, quantified water shortages to each of the three environmental flow cases, and explored the effects of different water management alternatives on improving instream flows. To address these particular questions, the environmental water use was assigned the lowest priority to ensure that agricultural water users are allocated water prior to instream flow. Model testing of predictive accuracy with NSE values described previously were calculated for baseline model runs for each water year type. A NSE value of 1 indicates a perfect match between modeled and observed discharge. The following NSE values were calculated for each water year type with water year in parentheses: Critically Dry (2008), NSE = 0.92; Dry (2009), NSE = 0.96; Below Normal (2010), NSE = 0.87; Above Normal (2005), NSE = 0.86; Wet (2006), NSE = Figure 8 shows modeled outflow in lower Mill Creek for the critically dry water year 2008 with baseline water management. The modeled flow regime remains nearly unaltered during the winter and diminishes starting on April 1 st (week 27) till October 31 st (week 5) corresponding to the irrigation season. Observed outflows at the DWR MCH stream gauge show a similar pattern of winter season unaltered flow with noticeable surface water abstractions starting on April 1 st and ending in mid-october (week 3) (Figure 8). 25

32 Figure 8. Modeled and observed lower Mill Creek outflow for water year 2008 with baseline water management (NSE = 0.92). Fish Passage Case The fish passage case was intended to provide flows at critical times of year. Figure 9 shows water allocation to environmental fish passage flows for critically dry water year During the fall, October 15 th through the first week of November, water year weeks 3 to 5 have insufficient water to meet upstream migration passage flow requirements after agricultural diversions. Similar conditions exist in the spring, where weeks 36 through 39 (approximately June 9 th to 29 th ) have insufficient water for spring-run Chinook salmon and steelhead trout downstream outmigration. 26

33 Figure 9. Fish passage environmental flow allocations and total water diversions for water year 2008 with baseline water management. Over the critically dry water year 2008, total annual water shortage to fish passage flow requirements is 3.0 million cubic meters (mcm), roughly 2400 acre-feet (Figure 10). The shortages to fish passage flows occur in two main periods: 2.1 mcm (1700 acre-feet) during the fall and 0.9 mcm (700 acre-feet) in the spring. The fall shortage volume of 2.1 mcm (1700 acre-feet) was also found for below the normal water year and decreased to 1.7 mcm (1400 acre-feet) for the wet water year. 27

34 Figure 10. Fish passage environmental flow shortages for critically dry water year 2008 with baseline water management. Figure 11 shows fish passage flows water shortages for three different water year types (critically dry, below normal, and wet) and the different water management alternatives (baseline, 4 conjunctive use wells, water exchange agreement, a combination of wells and water exchange agreement, and water rights purchases). Annual environmental shortage drops from 3.0 mcm (2400 acre-feet) in critically dry water year 2008 to 2.1 mcm (1700 acre-feet) in below normal water year 2010 and 2.0 mcm (1600 acre-feet) in wet water year The model indicates water shortage for fall fish passage flows during the last two weeks of October and the first week of November for all water year types from critically dry to wet for baseline water management. The spring shortages during weeks 36 to 39 present in critically dry water year 2008 are not present in the below normal and wet water years. 28

35 Figure 11. Fish passage shortages for critically dry (2008), below normal (2010), and wet (2006) water year types for five water management alternatives: baseline, 4 wells, water agreement, water agreement and 4 wells, and leaving Droz and Orange Cove instream. The x-axis corresponds to water year weeks and the y-axis correspond to water volume shortages in mcm. 29

36 Figure 12 shows the percentage decrease in fish passage flow shortages for the four water management options compared to baseline during critically dry water year The Droz and Orange Cove water transfer has the smallest reduction in annual environmental shortage of 31%. The four conjunctive use wells reduced annual shortage by 61%, while the water exchange agreement had a reduction of 41% from baseline. When only considering the fall fish passage period, the exchange agreement reduces shortages by about 60% compared to about 50% for the four wells. Finally, the combination of four wells and water exchange agreement nearly eliminated total annual water shortage. This alternative resulted in a shortage of 0.2 mcm (160 acre-feet) compared to the 3.0 mcm (2400 acre-feet) baseline shortage, with a reduction of 94%. Figure 12. Percent change of fish passage flow shortages for different water management alternatives compared to baseline for critically dry water year Below normal water year 2010 and wet water year 2006 both only showed shortages during the fall passage season and had similar reductions in shortages from each management alternative. 30

37 For the below normal water year, the Droz and Orange Cove water transfer reduced shortages by 16%, the four wells 50%, the exchange agreement 60%, with the well and exchange agreement combination reducing 100% of shortages (ffigure 13). In the wet water year, the management alternatives performed similarly with the following shortage reductions: Droz and Orange Cove (18.2%), four wells (52%), exchange agreement (62%), and elimination of all shortages with the wells and exchange agreement combination (Figure 14). Figure 13. Percent change of fish passage flow shortages for different water management alternatives compared to baseline for below normal water year

38 Figure 14. Percent change of fish passage flow shortages for different water management alternatives compared to baseline for wet water year Minimum Instream Flow Case A minimum instream flow of 2.55 cms (90 cfs) was run in the model to see how water management actions can improve a more broad-based environmental flow requirement to support a set of focal freshwater species in addition to anadromous salmonids. Figure 15 shows results of model runs with the same water management alternatives explored above with an additional water rights purchase of LMMWC water rights. The baseline condition experiences an annual shortage of 30.9 mcm (25,000 af) for critically dry water year 2008, and decreases to 20.9 mcm (16,900 af) for below normal water year 2010 and 18.7 mcm (15,200 af) for wet year Critically dry year 2008 has environmental shortages of 6.8 mcm (5500 af) during weeks 1 through 5, 1.1 mcm (890 af) during weeks 27 and 28, and 23.0 mcm (18,600 af) in weeks 35 through 52. Similar results were found for below normal water year Fall shortages during weeks 1 through 5 were 6.9 mcm (5600 af), with shortages beginning later in spring starting with 32

39 week 42 for a spring shortage volume of 14.0 mcm (11,300 af). Wet water year 2006 showed the same period (weeks 1-5) and volume (6.8 mcm) of water shortage in the fall as However, late spring shortages begin 8 weeks later starting in week 43 in late July with a shortage volume of 11.9 mcm (9,600 af). The option of purchasing the largest water rights holder in the system, LMMWC, gave the largest decrease in annual environmental flow volume shortage for critically dry water year 2008 with a decrease of 86% from baseline from 30.9 mcm to 4.3 mcm (Figure 16). The four wells decreased environmental shortages by 28% and the combination of the four wells and the water exchange agreement had a 24% environmental shortage reduction. The Droz and Orange Cove water rights purchases had the smallest shortage decrease of 10%. The water exchange agreement alone increases environmental flow shortages in the spring and summer months when TNC water rights are made available for irrigation, which increase annual environmental shortage for minimum instream flows by 3 percent. The results for the below normal and wet water years show the same order, with LMMWC as the only option that gets close to eliminating minimum instream flow shortages (Table 3). 33

40 Figure 15. Minimum instream flow shortages for critically dry (2008), below normal (2010), and wet (2006) water years for baseline, 4 wells, water exchange agreement, agreement and 4 wells, Droz and Orange Cove left instream, and LMMWC water left instream. The x-axis corresponds to water year weeks and the y-axis corresponds to water volume shortages in mcm. 34

41 Figure 16. Percent change of minimum instream flow shortages for different water management alternatives compared to baseline for critically dry water year Sustainability Boundary Approach Case Figure 17 shows modeled shortages for an 80 percent sustainability boundary approach environmental target case. For critically dry water year 2008, weeks 1 through 5 have a shortage of 6.7 mcm (5400 af) and weeks 27 through 52 have a shortage of 43.2 mcm (35,000 af) for a total annual shortage of 49.9 mcm (40,000 af). Below normal water year 2010 experiences shortages during the same weeks with a smaller volume, 6.4 mcm (5200 af) for the fall and 41.9 mcm (34,000 af) for the spring and summer for a total annual shortage of 48.3 mcm (39,000 af). Wet water year 2006 has shortages during the same weeks 1 through 5 of 7.2 mcm (5800 af) with spring shortages starting in week 30 through 52 of 35.1 mcm (28,000 af) for an annual shortage of about 42.4 mcm (34,000 af). 35

42 Figure 17. SBA environmental shortages for critically dry (2008), below normal (2010), and wet (2006) water years for baseline, 4 wells, agreement, agreement and 4 wells, Droz and Orange Cove purchase, and LMMWC purchase management options. The x-axis is in water year weeks and the y-axis is water volume shortages in mcm. 36

43 Effects of the different water management options to the SBA environmental flow case were similar to the MIF case with little variation between water year types. For critically dry water year 2008, the LMMWC water right purchase decreases environmental water shortage by 97% of base shortages, followed by a 21% decrease in environmental water shortages with the use of four conjunctive use wells, a 19% decrease with the four well and water exchange agreement combination, and an 8% decrease with the purchase of two water rights Droz and Orange Cove (Table 3). The exchange agreement alone increases environmental shortage by 2% of baseline. Figure 18. Percent change of 80% sustainability boundary approach flow shortages for different water management alternatives compared to baseline for critically dry water year

44 Table 3. Annual volume of shortages for fish passage, MIF, and SBA environmental flow cases by water year type and water management alternatives. Percent decrease in environmental flow shortage from baseline indicated in parentheses. Annual Volume of Environmental Flow Shortage (mcm) Fish Passage mcm (% decrease) 2.55 cms MIF mcm (% decrease) 80% SBA mcm (% decrease) WY 2008 Critically Dry Baseline Wells 1.2 (61%) 22.3 (28%) 39.3 (21%) Agreement 1.8 (41%) 31.9 (+3%) 39.3 (+2%) 4 Wells & Agreement 0.2 (94%) 23.3 (24%) 40.4 (19%) Droz & Orange Cove 2.1 (31%) 27.8 (10%) 45.9 (8%) LMMWC (86%) 1.7 (97%) WY 2010 Below Normal Baseline Wells 1.0 (50%) 15.4 (26%) 37.7 (22%) Agreement 0.8 (60%) 22.1 (6%) 50.2 (+4%) 4 Wells & Agreement 0.0 (100%) 16.7 (20%) 39.6 (18%) Droz & Orange Cove 1.7 (16%) 18.9 (9%) 43.9 (9%) LMMWC (92%) 1.1 (98%) WY 2006 Wet Baseline Wells 1.0 (52%) 13.5 (28%) 33.4 (21%) Agreement 0.7 (62%) 20.6 (11%) 45.0 (+6%) 4 Wells & Agreement 0.0 (100%) 15.2 (19%) 36.0 (15%) Droz & Orange Cove 1.6 (18%) 16.6 (11%) 38.5 (9%) LMMWC (99%) 0.7 (98%) 38

45 Discussion This study has found that late October is a critical period of water scarcity in the lower Mill Creek watershed, in which there is insufficient natural flow to meet all agricultural irrigation demands and environmental fish passage requirements. This finding persists in all SVI water year types from critically dry to wet. The fall fish passage shortages for all water year types is ranges from a volume of 1.7 to 2.1 mcm ( af). In contrast, the spring base flow requirements for fish passage experience shortage during the critically dry water year, but not for the below normal and wet water years. Since fall shortages occur during the last few weeks of irrigation, a potential solution water scarcity solution is to shift the irrigation period to begin earlier in the spring, though this depends on the feasibility and utility of early irrigation in the region. Model results indicate that a water exchange agreement coupled with 4 wells could decrease fish passage flow shortages by % (Table 3) with no curtailment to irrigation water supplies. This information can help managers develop and select water management options that need to for each water year condition. However, the frequency of water year types is unlikely to be static with climate change (Null and Viers 2013), so it will be necessary for water management policies to adapt to new conditions. Null and Viers found that the frequency of dry and critically dry years is likely to increase, which would increase scarcity and increase the likelihood of not meeting environmental flow targets. As target taxa are considered special status species, increased regulatory action to limit further jeopardy may result. Further, changing hydroclimatic conditions indicate more precipitation as rain, as opposed to snow, which will increase winter magnitudes, 39

46 limit snowmelt runoff, and increase low flow duration. This is likely to exacerbate environmental flow shortages during late summer, a period with consistent unmet environmental demands. Both the MIF and SBA environmental flow cases show that the only water management alternative able to decrease the environmental flow shortages by more than 80 percent of baseline is the purchase of the Los Molinos Mutual Water Company water rights, which are 68 percent of all total water rights in the system. Given the current water allocations in the system, substantial curtailment of irrigation may needed to meet these environmental flow objectives. This study developed and used a decision-support tool to quantify water scarcity periods through use of a linear programming model in an Excel spreadsheet. While model results have identified critical water scarcity periods and the effects of potential water management options in the Mill Creek case study, some limitations are important to keep in mind. For example, water quality parameters such as temperature are critical in supporting freshwater fish. In particular, the survival of migrating fish depends on having not only sufficient water quantity to traverse riffles but also water with temperature ranges appropriate for their physiology. While sufficient instream flows affect stream temperature, this work focused primarily on water volume, and it is recommended that future work address the potential effect of water transfers on water quality parameters appropriate for freshwater fish species. In addition, future work that couples the loss in agricultural revenue from water transfers can provide valuable insight on the economic costs of meeting environmental flow requirements in diversion-impacted rivers. Finally, due to the scope 40

47 of this project, groundwater and surface water interactions could not be thoroughly investigated and were not represented in the model. However, due to the alluvial nature of the valley reaches of lower Mill Creek, it is likely that groundwater surface water interactions are present in the system and future research should strive to address this issue. Conclusion This worked has demonstrated the development and use of a linear programming model to explore the effects of different water management options to meet instream environmental flow targets. Through its application to a case study on Mill Creek, late October and early November are a critical period of water scarcity for fish passage during all water year types. This fall passage period environmental shortage of 1.7 to 2.1 mcm ( af) can be reduced through water exchanges, wells, or shifting of the irrigation season. The output of the decision-support tool can help inform when water transfer agreements should be negotiated to meet fish passage flow requirements. Furthermore, this work can be extended to include a broader range of riparian species or ecosystem processes as well as the adoption of novel water resource infrastructure or irrigation methods. The model developed can be modified and applied to other river systems with flow regimes impaired by water abstractions, such as other watersheds in the Mount Lassen foothills such as Deer Creek as well as coastal rivers in Northern California subject to flow regime impairment through small diversions. 41