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.

Friends of the River v. Sites Project Authority

California Courts of Appeal, Third Appellate District | September 20th, 2024

From Sediment to Top Predators: Broad Exposure of Polyhalogenated Carbazoles in San Francisco Bay

American Chemical Society (ACS) | January 23rd, 2017

The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZs) contamination in an aquatic ecosystem. PHCZs have been found in soi

The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZs) contamination in an aquatic ecosystem. PHCZs have been found in soil and aquatic sediment from several different regions, but knowledge of their bioaccumulation and trophodynamics is extremely scarce. This work investigated a suite of 11 PHCZ congeners in San Francisco Bay (United States) sediment and organisms, including bivalves (n = 6 composites), sport fish (n = 12 composites), harbor seal blubber (n = 18), and bird eggs (n = 8 composites). The most detectable congeners included 3,6-dichlorocarbazole (36-CCZ), 3,6-dibromocarbazole (36-BCZ), 1,3,6-tribromocarbazole (136-BCZ), 1,3,6,8-tetrabromocarbazole (1368-BCZ), and 1,8-dibromo-3,6-dichlorocarbazole (18-B-36-CCZ). The median concentrations of ΣPHCZs were 9.3 ng/g dry weight in sediment and ranged from 33.7 to 164 ng/g lipid weight in various species. Biomagnification was observed from fish to harbor seal and was mainly driven by chlorinated carbazoles, particularly 36-CCZ. Congener compositions of PHCZs differed among species, suggesting that individual congeners may be subject to different bioaccumulation or metabolism in species occupying various trophic levels in the studied aquatic system. Toxic equivalent (TEQ) values of PHCZs were determined on the basis of their relative effect potencies (REP) compared to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The median TEQ was 1.2 pg TEQ/g dry weight in sediment and 4.8–19.5 pg TEQ/g lipid weight in biological tissues. Our study demonstrated the broad exposure of PHCZs in San Francisco Bay and their characteristics of bioaccumulation and biomagnification along with dioxin-like effects. These findings raise the need for additional research to better elucidate their sources, environmental behavior, and fate in global environments.

Gage Gap

Nature Conservancy | October 31st, 2018

Following a difficult five-year drought, California just had one of the wettest winters on record. The state is famous for its highly engineered water system, whi

Following a difficult five-year drought, California just had one of the wettest winters on record. The state is famous for its highly engineered water system, which moves millions of gallons of water from north to south and east to west. Thirty-nine million people and our $47 billion agricultural industry rely on that water, not to mention wildlife from the Sierra to the sea. And yet we have surprisingly little data about how much water is moving through our streams at any given time. There are over 3,600 locations in California where stream gages have been active at some point, but only 54% have been active recently. And even fewer of those provide the kind of rich, real-time reporting needed to manage what is arguably our state’s most precious and contentious resource.

Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary

University of California, Davis (UC Davis) | July 14th, 2022

Gill-net size selectivity for fifteen fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which togethe

Gill-net size selectivity for fifteen fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood. Selectivity curves are provided for each species to inform researchers about population characteristics of fishes sampled with similar gill nets.

Global impacts of marine heatwaves on coastal foundation species

Nature Portfolio (Springer Nature) | June 13th, 2024

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

While sometimes difficult to admit, perspectives of European and white males have overwhelmingly dominated fisheries science and management in the USA. This dynamic is ex

While sometimes difficult to admit, perspectives of European and white males have overwhelmingly dominated fisheries science and management in the USA. This dynamic is exemplified by bias against “rough fish”—a pejorative ascribing low-to-zero value for countless native fishes. One product of this bias is that biologists have ironically worked against conservation of diverse fishes for over a century, and these problems persist today. Nearly all U.S. states retain bag limits and other policies that are regressive and encourage overfishing and decline of native species. Multiple lines of evidence point towards the need for a paradigm shift. These include: (1) native species deliver critical ecosystem services; (2) little demonstration that native fish removals deliver intended benefits; (3) many native fishes are long-lived and vulnerable to overfishing and decline; and (4) fisher values and demographics shifting towards native fish conservation. Overall, existing native fish policies are unacceptable and run counter to the public trust doctrine where government agencies manage natural resources for public use. We encourage agencies to revisit their policies regarding native fishes and provide suggestions for developing more holistic, protective, and inclusive conservation policy.

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.