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.

Gut Contents Analysis of Four Fish Species Collected in the San Leandro Bay RMP PCB Study in August 2016

San Francisco Estuary Institute (SFEI) | November 7th, 2018

In support of PCB modeling for San Leandro Bay, a Priority Margin Unit (PMU) for PCB load reduction in the estuary, fish samples of four species (topsmelt, shiner perch,

In support of PCB modeling for San Leandro Bay, a Priority Margin Unit (PMU) for PCB load reduction in the estuary, fish samples of four species (topsmelt, shiner perch, white croaker, and northern anchovy ) were obtained in August 2016 for both tissue analysis and examination of gut contents. The bay was sampled at eight locations, with a repeated sampling at one location (Airport Lagoon) for one species (topsmelt). Fish were measured, weighed, and dissected, and their gut contents examined microscopically. Topsmelt (9 samples, 188 specimens) had the greatest variety of food items, with gammarid amphipods and chain diatoms predominating. Some topsmelt, especially larger individuals, consumed macroalgae as a major dietary component. Two samples at two sites for shiner perch (20 fish each) had contents composed of close to 50% gammarids at both sites, but differed in proportions of bivalves and polychaetes among the important food items. The one sample of white croaker had consumed mostly gammarids, with fish and polychaetes ranking next in importance. A single sample of northern anchovy (20 fish analyzed) differed radically from the other species in consuming mainly a diatom that appears to have been filtered from the water column. Trace amounts of plastic fiber were seen in all species except shiner perch. All exposure to sediment appeared to have occurred in the top 2 cm of the sediment column, or as contact with flocculent material on plants or hard substrates, or even in the water column, as some fine sand grains were seen in all fish, even anchovy. There was no conclusive evidence of site-specific foraging (site fidelity). The best spatial coverage was for topsmelt, and these fish appear to have fed opportunistically, with some evidence for having fed outside San Leandro Bay.

Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for Tidal Restoration

University of California, Davis (UC Davis) | December 1st, 2022

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restorati

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restoration actions that reverse habitat loss, can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass (Morone saxatilis; 63 to 671 mm standard length; estimated age 1 to 5 yrs) in the San Francisco Estuary during spring and summer in three habitat types—marsh, shoal, and channel—with the marsh habitat type serving as a model for ongoing and future restoration. Based on a preyspecific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~ 40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly because of the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Ecological Society of America (Wiley) | January 13th, 2023

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.