French Creek Flow Accounting Study

Scott River Water Trust | May 15th, 2020

The Scott River Water Trust (SRWT) has been working with adjudicated water-users in Scott Valley since 2007 to develop opportunities for stream flow enhancement through t

The Scott River Water Trust (SRWT) has been working with adjudicated water-users in Scott Valley since 2007 to develop opportunities for stream flow enhancement through temporary leases or long-term/permanent dedications of surface water rights. Under the seasonal Water Leasing Program, the SRWT contracts with voluntary agricultural producers to temporarily forbear all or part of their decreed water right(s) during the irrigation season in exchange for fair financial compensation. The purpose of the seasonal Water Leasing Program is to improve conditions for anadromous fish in priority stream reaches during critical life stages and time periods. The Siskiyou Resource Conservation District (SRCD) has been integrally involved with implementation of the seasonal Water Leasing Program since its inception and particularly with the monitoring component. Monitoring of seasonal transactions is generally limited to ensuring compliance with the lease terms and confirming stream response. However, in 2016 the SRWT proposed expanding the scope of effectiveness monitoring associated with the Water Leasing Program based on suggestions from Andrew Purkey and Rankin Holmes of the National Fish and Wildlife Foundation and their experience monitoring transactions in the Columbia River Basin (Holmes, et al., 2013). Under funding from the California Flow Restoration Accounting Fund managed by the National Fish and Wildlife Foundation, the SRWT contracted with the SRCD to explore several additional effectiveness monitoring techniques on French Creek including instream water level/discharge monitoring, wetted- perimeter analysis and alluvial connectivity surveillance. The purpose of this additional monitoring was to evaluate the applicability and effectiveness of these techniques to stream flow enhancement in Scott Valley and determine whether it would make sense for the SRWT adopt these practices into its programs. The specific components and objectives of the work completed on French Creek included: • Evaluate the instream effect of forbearance agreements performed by SRWT • Establish and maintain monitoring stations throughout French Creek to determine the downstream extent that returned water from various leases had on stream flow and temperature • Perform wetted perimeter analysis on French Creek to develop a relationship between instream flows and aquatic habitat conditions • Conduct periodic fisheries surveys through French Creek to evaluate the relative abundance of salmonids influenced by the transactions • Conduct periodic foot surveys through lower French Creek to establish the temporal and spatial connectivity to the Scott River This report summarizes the monitoring and analysis conducted by the SRCD during the 2018 and 2019 water leasing seasons under the French Creek Flow Accounting Study and provides conclusions related to the applicability of these methods to the SRWT.

From the Sierra to the Sea: The Ecological History of the San Francisco Bay-Delta Watershed

Bay Institute | January 1st, 1998

A vast watershed connects the mountain streams surrounding California’s Central Valley with San Francisco Bay and the ocean beyond. Over the course of the last two cent

A vast watershed connects the mountain streams surrounding California’s Central Valley with San Francisco Bay and the ocean beyond. Over the course of the last two centuries, much of the natural productivity, biodiversity and ecological integrity of the watershed has been destroyed by modifying the environment without fully understanding the long-term environmental consequences. Long the site of some of the nation’s most intensive conflicts over the use of land and water resources, this system is now emerging as the focus of one of the most ambitious ecological restoration efforts ever undertaken in the United States. This report was designed to provide a coherent and defensible ecological framework and information base for restoration. The need for such an historical, broad-scale perspective on system ecology stems from two fundamental principles of ecological restoration - the need to manage toward a natural template and to manage at ecosystem and landscape levels.

Gillnet Sampling Methods for Monitoring Status and Trends of Clear Lake Hitch in Clear Lake, Lake County, California

U.S. Geological Survey (USGS) | May 2nd, 2025

The Clear Lake Hitch (Lavinia exilicauda chi) is a minnow endemic to Clear Lake, Lake County, California. This species is listed as a threatened species under the Califor

The Clear Lake Hitch (Lavinia exilicauda chi) is a minnow endemic to Clear Lake, Lake County, California. This species is listed as a threatened species under the California Endangered Species Act and has been petitioned for listing under the United States Endangered Species Act. In 2017, the U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, initiated a Clear Lake Hitch monitoring program to generate information annually on relative abundance and size structure.

Gone with the flow

Bay Institute | August 1st, 2010

The Bay Institute's primer Gone with the Flow describes in plain language how runoff flowing from the mountain watersheds ringing California’s Central Valley provided c

The Bay Institute's primer Gone with the Flow describes in plain language how runoff flowing from the mountain watersheds ringing California’s Central Valley provided coldwater paradises for salmon returning to their native streams; turned lowland rivers and their floodplains into a rich source of food and shelter for young fish; mingled in the Delta’s complex maze of marshes and sloughs; and created a vast expanse of brackish water habitat essential for estuarine creatures in the upper reaches of San Francisco Bay. The primer also explains how the lack of access to most upland streams now forces migratory fish to cope with undesirable, often lethal flow conditions; how runoff in lowland rivers has been shifted from spring to summer, or even almost completely cut off in the San Joaquin basin, with disastrous consequences for the environment; how reverse flows in Delta channels kill hundreds of millions of aquatic organisms each year; and how the Bay is now in a permanent ecological drought because of the diversion of half its freshwater inflow.

Goodbye to “Rough Fish”: Paradigm Shift in the Conservation of Native Fishes

American Fisheries Society (AFS) | July 21st, 2021

Groundwater Characterization and Effects of Pumping in the Death Valley Regional Groundwater Flow System, Nevada and California, with Special Reference to Devils Hole

U.S. Geological Survey (USGS) | March 5th, 2020

Groundwater flow and development were characterized in four groundwater basins of the Death Valley regional flow system in Nevada and California with calibrated, groundwa

Groundwater flow and development were characterized in four groundwater basins of the Death Valley regional flow system in Nevada and California with calibrated, groundwater-flow models. Natural groundwater discharges in the Furnace Creek, Lower Amargosa, and Saratoga Spring areas were defined and distributed consistently with a revised hydrogeologic framework. This simplified hydrogeologic framework was limited to four hydraulically unique, hydrogeologic units: (1) basin fill; (2) carbonate rocks; (3) volcanic rocks; and (4) low-permeability granitic and siliciclastic rocks. Hydrogeologic units and division of carbonate and volcanic rocks between shallow and deep were supported by results from 271 aquifer tests and specific-capacity estimates. Greater than 90 percent of field-estimated transmissivity occurred within 1,600 feet (ft) of the water table. Pumping in the study area from 1960 to 2010 averaged 46,000 acre-feet per year (acre-ft/yr), which is 80 percent of the predevelopment discharge. The central Amargosa Desert and Pahrump Valley were the two primary pumping centers and measurably affected water levels across 900 square miles in 2018. Water levels in Devils Hole were a special focus because endangered Devils Hole pupfish (Cyprinodon diabolis) are affected by water-level declines. Pumping 42,100 acre-ft by Cappaert Enterprises, formerly Spring Meadows, Inc., caused a 2.3-ft water-level decline in Devils Hole, which temporarily reduced habitat of Devils Hole pupfish by 85 percent in 1972. If no pumping occurred, water levels in Devils Hole would have risen naturally about 1 ft between 1973 and 2018 from temporal variations in recharge. The 2.6-ft range of measured water-level changes in Devils Hole was simulated with a root-mean-square error of 0.2 ft during the 70-year period of record. Simulated water-level declines from pumping totaled 1.4 ft in 2018, with 25 and 34 percent attributed to pumping by Cappaert Enterprises and the central Amargosa Desert, respectively. Water levels in Devils Hole will decline at rates of 0.1–0.2 ft per decade if pumping from Ash Meadows groundwater basin and the central Amargosa Desert continue at current rates. Effects of future natural water-level fluctuations remain unknown. Ash Meadows and Alkali Flat–Furnace Creek Ranch groundwater basins are hydraulically connected near well AD-4, about 5 miles south of the town of Amargosa Valley, Nevada. About 40 percent of the discharge from the Furnace Creek area is recharged in the Ash Meadows groundwater basin. Basin fill in the central Amargosa Desert hydraulically connects carbonate rocks east of well AD-4 with saturated carbonate rocks in the Funeral Range. About 7 percent of the 960,000 acre-ft pumped from Ash Meadows and Alkali Flat–Furnace Creek Ranch groundwater basins prior to 2019 was captured discharge from springs and phreatophytes. Greater than 40 percent of the 2,080,000 acre-ft pumped from Pahrump Valley between 1910 and 2019 was capture that primarily discharged from Bennetts and Manse Springs. Simulated advective-flow distances and velocities from underground nuclear tests are within the range of advective transport calculations from tritium data and previous radionuclide transport investigations. Boundary conditions and flow rates from the regional model in this study are plausible for local-scale flow and radionuclide transport models. Simulated 165-year groundwater-flow paths do not extend into pumping areas and effects of regional pumping on advective transport are negligible.

Groundwater Simulation and Management Models for the Upper Klamath Basin, Oregon and California

U.S. Geological Survey (USGS) | May 5th, 2012

The upper Klamath Basin encompasses about 8,000 square miles, extending from the Cascade Range east to the Basin and Range geologic province in south-central Oregon and n

The upper Klamath Basin encompasses about 8,000 square miles, extending from the Cascade Range east to the Basin and Range geologic province in south-central Oregon and northern California. The geography of the basin is dominated by forested volcanic uplands separated by broad interior basins. Most of the interior basins once held broad shallow lakes and extensive wetlands, but most of these areas have been drained or otherwise modified and are now cultivated. Major parts of the interior basins are managed as wildlife refuges, primarily for migratory waterfowl. The permeable volcanic bedrock of the upper Klamath Basin hosts a substantial regional groundwater system that provides much of the flow to major streams and lakes that, in turn, provide water for wildlife habitat and are the principal source of irrigation water for the basin’s agricultural economy. Increased allocation of surface water for endangered species in the past decade has resulted in increased groundwater pumping and growing interest in the use of groundwater for irrigation. The potential effects of increased groundwater pumping on groundwater levels and discharge to springs and streams has caused concern among groundwater users, wildlife and Tribal interests, and State and Federal resource managers. To provide information on the potential impacts of increased groundwater development, and to aid in the development of a groundwater management strategy, the U.S. Geological Survey, in collaboration with the Oregon Water Resources Department and the Bureau of Reclamation, has developed a groundwater model that can simulate the response of the hydrologic system to these new stresses. The groundwater model was developed using the U.S. Geological Survey MODFLOW finite-difference modeling code and calibrated using inverse methods to transient conditions from 1989 through 2004 with quarterly stress periods. Groundwater recharge and agricultural and municipal pumping are specified for each stress period. All major streams and most major tributaries for which a substantial part of the flow comes from groundwater discharge are included in the model. Groundwater discharge to agricultural drains, evapotranspiration from aquifers in areas of shallow groundwater, and groundwater flow to and from adjacent basins also are simulated in key areas. The model has the capability to calculate the effects of pumping and other external stresses on groundwater levels, discharge to streams, and other boundary fluxes, such as discharge to drains. Historical data indicate that the groundwater system in the upper Klamath Basin fluctuates in response to decadal climate cycles, with groundwater levels and spring flows rising and declining in response to wet and dry periods. Data also show that groundwater levels fluctuate seasonally and interannually in response to groundwater pumping. The most prominent response is to the marked increase in groundwater pumping starting in 2001. The calibrated model is able to simulate observed decadal-scale climate-driven fluctuations in the groundwater system as well as observed shorter-term pumping-related fluctuations. Example model simulations show that the timing and location of the effects of groundwater pumping vary markedly depending on the pumping location. Pumping from wells close (within a few miles) to groundwater discharge features, such as springs, drains, and certain streams, can affect those features within weeks or months of the onset of pumping, and the impacts can be essentially fully manifested in several years. Simulations indicate that seasonal variations in pumping rates are buffered by the groundwater system, and peak impacts are closer to mean annual pumping rates than to instantaneous rates. Thus, pumping effects are, to a large degree, spread out over the entire year. When pumping locations are distant (more than several miles) from discharge features, the effects take many years or decades to fully impact those features, and much of the pumped water comes from groundwater storage over a broad geographic area even after two decades. Moreover, because the effects are spread out over a broad area, the impacts to individual features are much smaller than in the case of nearby pumping. Simulations show that the discharge features most affected by pumping in the area of the Bureau of Reclamation’s Klamath Irrigation Project are agricultural drains, and impacts to other surface-water features are small in comparison. A groundwater management model was developed that uses techniques of constrained optimization along with the groundwater flow model to identify the optimal strategy to meet water user needs while not violating defined constraints on impacts to groundwater levels and streamflows. The coupled groundwater simulation-optimization models were formulated to help identify strategies to meet water demand in the upper Klamath Basin. The models maximize groundwater pumping while simultaneously keeping the detrimental impacts of pumping on groundwater levels and groundwater discharge within prescribed limits. Total groundwater withdrawals were calculated under alternative constraints for 2 Groundwater Simulation and Management Models for the Upper Klamath Basin, Oregon and California drawdown, reductions in groundwater discharge to surface water, and water demand to understand the potential benefits and limitations for groundwater development in the upper Klamath Basin. The simulation-optimization model for the upper Klamath Basin provides an improved understanding of how the groundwater and surface-water system responds to sustained groundwater pumping within the Bureau of Reclamation’s Klamath Project. Optimization model results demonstrate that a certain amount of supplemental groundwater pumping can occur without exceeding defined limits on drawdown and stream capture. The results of the different applications of the model demonstrate the importance of identifying constraint limits in order to better define the amount and distribution of groundwater withdrawal that is sustainable.

Guidelines for salmonid passage at stream crossings

National Marine Fisheries Service (NMFS) | August 20th, 2013

This document provides guidelines for design of stream crossings to aid upstream and downstream passage of migrating salmonids. It is intended to facilitate the design of

This document provides guidelines for design of stream crossings to aid upstream and downstream passage of migrating salmonids. It is intended to facilitate the design of a new generation of stream crossings, and assist the recovery of threatened and endangered salmon species. These guidelines are offered by the National Marine Fisheries Service, Southwest Region (NMFS-SWR), as a result of its responsibility to prescribe fishways under the Endangered Species Act, the Magnuson-Stevens Act, the Federal Power Act, and the Fish and Wildlife Coordination Act. The guidelines apply to all public and private roads, trails, and railroads within the range of anadromous salmonids in California.

Hydrology and Hydrodynamics on the Sacramento River Near the Fremont Weir, California—Implications for Juvenile Salmon Entrainment Estimates

U.S. Geological Survey (USGS) | November 9th, 2018

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the weir to increase access to the Yolo Bypass, a seasonal floodplain of the Sacramento River. Detailed hydrodynamic and velocity measurements were made at a river bend near the Fremont Weir in the winter and spring of 2016 to examine backwater conditions and estimate the hydraulic entrainment zone, a zone where fish would be predicted to be entrained into the notch. Secondary circulation near the river bend was shown to shift the velocity and discharge distributions toward the outside of the bend. Variability in the stage-discharge relation was shown to be the biggest source of uncertainty in determining the location of the hydraulic entrainment zone. Outflow from the Sutter Bypass and high flow on the Feather River resulted in backwater conditions near the Fremont Weir about 25 percent of the time over the 27-year period from April 1990–April 2017. Velocity measurements used to estimate the critical streakline position (the outer edge of the hydraulic entrainment zone) were not made over a sufficient range of conditions to explicitly quantify the variability in the location of the critical streakline. The variability in the critical streakline position was therefore represented stochastically with a random effects model. The estimated position of the critical streakline and the random effects model are input parameters used in a simulation designed to estimate fish entrainment over a 15-year period. The estimates of the critical streakline and likely fish entrainment could be much improved with velocity measurements over a broader range of stage and discharge conditions. 

Hydrology, Ecology, and Fishes of the Klamath River Basin (2008)

National Academy of Sciences (NAS) | January 1st, 2008

The Klamath River basin, which spans parts of southern Oregon and northern California, has been the focus of a prominent conflict over competing uses for water. Manag

The Klamath River basin, which spans parts of southern Oregon and northern California, has been the focus of a prominent conflict over competing uses for water. Management actions to protect threatened and endangered fish species in the basin have left less water available for irrigation in dry years and heightened tensions among farmers and other stakeholders including commercial fishermen, Native Americans, conservationists, hunters, anglers, and hydropower producers. This National Research Council report assesses two recent studies that evaluate various aspects of flows in the Klamath basin: (1) the Instream Flow Phase II study (IFS), conducted by Utah State University, and (2) the Natural Flow of the Upper Klamath Basin study (NFS), conducted by the U.S. Bureau of Reclamation (USBR). The report concludes that both studies offer important new information but do not provide enough information for detailed management of flows in the Klamath River, and it offers many suggestions for improving the studies. The report recommends that a comprehensive analysis of the many individual studies of the Klamath river basin be conducted so that a big picture perspective of the entire basin and research and management needs can emerge. Key Messages If these conclusions were borne out by studies incorporating experimental flows and monitored responses, managers would be able to have greater confidence that decisions to increase flows would have a beneficial effect on anadromous fishes in the lower river The Instream Flow Study Phase II did not include important water-quality attributes, such as dissolved oxygen levels, nutrient loadings, contaminants, and sediment concentrations, although each has important implications for the vitality of the fish populations of the Klamath River. The Natural Flow Study and the Instream Flow Study Phase II were major science and engineering investigations, but the linkage of one to the other was only partially achieved. The Natural Flow Study was seriously compromised by several fundamental issues, including its choice of a basic approach for understanding natural flows, choices of the models for calculations, and serious omissions of factors likely to influence river flows at the Iron Gate Dam gauge site. The basin and its biota have changed so much in the past century that the implications for the fishes of restoring natural flows are not clear. The committee concluded that the Natural Flow Study includes calculated flows that are at best first approximations to useful estimates of such flows. The committee found important shortcomings in the Instream Flow Study Phase II and its use of various models and data. Two major shortcomings use of monthly data and lack of tributary analyses are so severe that that they should be addressed before decision makers can use the outputs of the study to establish precise flow regimes with confidence. The most important outcome of the Instream Flow Study was that it indicated that increases in existing flows downstream from Iron Gate Dam probably would benefit fish populations through improved physical habitat associated with more water and through reduced water temperatures. There was a lack of a thorough assessment of the relationship between flow-data time series and the behavior of different species and life stages and the population dynamics of coho and Chinook salmon When the science needs for the basin are better characterized, the individual studies necessary to create a sound science-based body of knowledge for decision makers and managers will be more easily identified. current flow regime. These are improvements in flow because they include intra- and inter-annual variations and probably will enhance Chinook salmon growth and young-of-the-year production. is not possible to know how well the recommendations apply to any one species or to all the species as a whole. Indeed, most of the information was from Chinook salmon, which suggests that confidence in its applicability to that species would be greater than to other species. of the representativeness of the reaches used for detailed study, and the statistical approach to analyze the calculated set of instream flows did not use normalized data and did not have provisions for identifying serial autocorrelations.