Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery (2003)

National Academy of Sciences (NAS) | January 1st, 2004

Instead of focusing primarily on how water levels and flows affect endangered and threatened fish in Oregon's Upper Klamath Lake and the Klamath River -- which run fr

Instead of focusing primarily on how water levels and flows affect endangered and threatened fish in Oregon's Upper Klamath Lake and the Klamath River -- which run from the lake in Oregon through northern California before emptying into the Pacific -- the federal agencies charged with protecting the fish should focus on other kinds of initiatives, such as removal of migration obstacles, prevention of entrainment by water management structures, improvement and creation of habitat, and reduction of summer water temperatures in tributaries. Key Messages The committee found some proposed actions as given in the 2001 biological opinions to lack substantial scientific support. In their biological opinions of 2002, the listing agencies appear to have resolved this issue either by obtaining concessions from USBR through mechanisms that are generally consistent with USBR?s goal of delivering irrigation water. Adaptive management is accepted in principle by the listing agencies but has not been implemented in the Klamath basin for the benefit of the listed species, except as part of the Trinity River Restoration Project. Although suckers of all age classes are present in Upper Klamath Lake, population densities of suckers are low, and there are no signs that the populations are returning to their previously high abundance. An alternate hypothesis is that an unusual combination of temperature, flow, and migration conditions occurred in 2002, possibly in association with weather that prevented the river from showing nocturnal cooling to an extent that would usually be expected. Barriers to passage caused by dams and diversion structures are important to coho salmon. The main-stem dams on the Klamath River block spawning movements, as do Dwinnell Dam on the upper Shasta River and the Trinity River Diversion project on the Trinity River. Dams also have contributed to habitat degradation. CDFG has proposed that the shape of the channel in the lowermost reaches of the Klamath main stem changed in 1997?1998 under the influence of high flows, which caused fish entering the river to be unable to proceed upstream under low-flow conditions. Causes of extreme temperatures include diversion of cold flows for use in agriculture, flow depletion that leads to warming of cool water, and destruction of riparian vegetation that leads to loss of shading. Coho habitat has been seriously degraded in the tributaries. Lack of cover and impairment of substrate through deposition of sediments are common. Woody debris, which is critical as cover for young fish, has largely been lost as a result of human activity. Excessive depletion of flow may separate fish from adequate habitat in the last half of summer. Coho salmon, unlike Chinook salmon, remain in freshwater for an entire year, during which they mainly occupy tributaries, where summer water temperatures can be dangerously high. Decrease in main-stem temperatures by augmentation of main-stem flows is problematic because augmentation water must be derived from the surface layer of Iron Gate Reservoir, which is very warm in summer. During the second half of September 2002, numerous fish died in the lowermost 40 mi of the Klamath River main stem, 150 mi below Iron Gate Dam. Most of the dead fish were adult Chinook salmon that had just entered the lower Klamath River. If a lasting change in channel configuration was responsible, recurrence of the episode can be expected with similar low flows in the future. If other factors were responsible, recurrence may be much less likely. It is unclear what the effect of specific amounts of additional flow drawn from controllable upstream sources (waters from reservoirs on the Trinity River or Iron Gate Reservoir) would have been. Information collected through monitoring and research has been valuable, but the absence of an integrated, evolving management plan connected to monitoring, research, review, and periodic readjustment of management actions will hamper progress in the future. Mass mortality of large fish in Upper Klamath Lake has occurred for many decades, but anthropogenic factors, especially those leading to strong dominance of Aphanizomenon, probably have increased its severity and frequency. Poor water quality may also challenge the sucker populations in other ways. High pH, for example, could be harmful to young fish even if they are not subject to the mass mortality of larger fish. No obvious explanation of the fish kill based on unique flow or temperature conditions is possible. Nonnative fishes, which are diverse and abundant in Upper Klamath Lake, may be suppressing the populations of endangered suckers there, but no practical mechanisms for reducing their abundance are known. Reservoirs of the main stem Klamath have created new habitat capable of holding endangered suckers, but recruitment of young fish has not been observed. Reservoirs have low potential to support self-sustaining populations. The fish kill, although important for Chinook salmon, did not involve many coho salmon (about 1% of the total dead fish) because coho enter the river later than Chinook, and thus were mostly absent when conditions leading to mass mortality occurred. The immediate cause of death was massive infection by two types of pathogens that are widely distributed and generally become harmful to fish under stress, particularly if crowding occurs. The most important cause of impairment of coho salmon probably is excessively high summer temperatures in tributary waters. There is no evidence of a causal connection between water level and water quality or fish mortality over the broad operating range in the 1990s, the period for which the most complete data are available for Upper Klamath Lake. Neither mass mortality of fish nor extremes of poor water quality shows any detectable relationship to water level.

Endangered and Threatened Species: Status for the San Francisco Bay-Delta Distinct Population Segment of the Longfin Smelt

U.S. Fish and Wildlife Service (FWS) | February 27th, 2023

Endangered Species Status for the San Francisco Bay-Delta Distinct Population Segment of the Longfin Smelt

U.S. Fish and Wildlife Service (FWS) | July 30th, 2024

We, the U.S. Fish and Wildlife Service (Service), determine endangered species status under the Endangered Species Act of 1973, as amended (Act), for the San Francisco Ba

We, the U.S. Fish and Wildlife Service (Service), determine endangered species status under the Endangered Species Act of 1973, as amended (Act), for the San Francisco Bay-Delta distinct population segment (DPS) of longfin smelt (Spirinchus thaleichthys), a fish species of the Pacific Coast. This rule extends the protections of the Act to this DPS and adds it to the List of Endangered and Threatened Wildlife.... This final rule is available on the internet at https://www.regulations.gov. Comments and materials we received on the proposed rule are available for public inspection at https://www.regulations.gov at Docket No. FWS-R8-ES-2022-0082. Availability of supporting materials: Supporting materials we used in preparing this rule, such as the species status assessment report, are available at https://www.regulations.gov at Docket No. FWS-R8-ES-2022-0082.

Ensuring the Public Trust

University of California, Davis (UC Davis) | July 1st, 2012

The California Supreme Court's recognition of the public trust doctrine as an integral part of California's water rights system was one of the momentous events in the h

The California Supreme Court's recognition of the public trust doctrine as an integral part of California's water rights system was one of the momentous events in the history of California (if not United States) environmental policy.' The court looked back to the foundational purposes of the public trust to hold that there are limits to the sovereign power to privatize the rights to use the waters of the state, and it looked forward to conclude that prudent development and sustainable use of California's water resources require the state to retain authority to protect the public trust for the benefit of all Californians. The court also defined the public trust as an environmental baseline that both protects the traditional interests of navigation, commerce, and fisheries and embodies the contemporary scientific and popular understanding that there are ecological limits to the diversion and use of water for consumptive purposes. The lessons of National Audubon Society v. Superior Court2 are now a commonplace of water rights law, appearing not just in administrative orders and judicial opinions, but also in standard water rights terms, policy studies, and legislation.

Environmental Characteristics of Select Managed Ponds in the Sacramento–San Joaquin Delta: Implications for Native Fish Conservation and Research

U.S. Geological Survey (USGS) | July 23rd, 2025

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpos

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt (Hypomesus transpacificus). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass (Micropterus salmoides) and black crappie (Pomoxis nigromaculatus) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

Environmental Law Foundation, et al. Plaintiffs and Respondents, v. State Water Resources Control Board, et al. Defendant, Cross-defendant and Respondent; County of Siskiyou, Defendant, Cross-complainant and Appellant

State of California | August 29th, 2018

Click here to read Brian Gray, Senior Fellow at the Public Policy Institute of California Water Policy Center and a Professor Emeritus at UC Hastings, on this ruling

Click here to read Brian Gray, Senior Fellow at the Public Policy Institute of California Water Policy Center and a Professor Emeritus at UC Hastings, on this ruling and the potential ramifications under the Sustainable Groundwater Management Act.

Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river

Environmental Biology of Fishes (Springer) | June 6th, 2008

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and floodplain habitats. Fish were placed in enclosures during times when wild salmon would naturally be rearing in floodplain habitats. We found significant differences in growth rates between salmon reared in floodplain and river enclosures. Salmon reared in seasonally inundated habitats with annual terrestrial vegetation experienced higher growth rates than those reared in a perennial pond on the floodplain. Growth of fish in the non-tidal river upstream of the floodplain varied with flow in the river. When flows were high, there was little growth and high mortality, but when the flows were low and clear, the fish grew rapidly. Fish displayed very poor growth in tidally influenced river habitat below the floodplain, a habitat type to which juveniles are commonly displaced during high flow events due to a lack of channel complexity in the main-stem river. Overall, ephemeral floodplain habitats supported higher growth rates for juvenile Chinook salmon than more permanent habitats in either the floodplain or river. Variable responses in both growth and mortality, however, indicate the importance of providing habitat complexity for juvenile salmon in floodplain reaches of streams, so fish can find optimal places for rearing under different flow conditions.

Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)

University of California, Davis (UC Davis) | December 1st, 2020

White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance because of a variety of factors. The purpose o

White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance because of a variety of factors. The purpose of our study was to identify the estuarine habitat used by White Sturgeon to aid in the conservation and management of the species locally and across its range. We seasonally sampled sub-adult and adult White Sturgeon in the central estuary using setlines across a habitat gradient representative of three primary structural elements: shallow wetland channel (mean sample depth = 2 m), shallow open-water shoal (mean sample depth = 2 m), and deep open-water channel (mean sample depth = 7 m). We found that the shallow open-water shoal and deep open-water channel habitats were consistently occupied by White Sturgeon in spring, summer, and fall across highly variable water quality conditions, whereas the shallow wetland channel habitat was essentially unoccupied. We conclude that sub-adult and adult White Sturgeon inhabit estuaries in at least spring, summer, and fall and that small, shallow wetland channels are relatively unoccupied.

Evaluating historical changes in a mussel bed community in northern California

Nature Portfolio (Springer Nature) | January 14th, 2025

Evaluating the hydrologic effects of the 2021–2022 Scott and Shasta irrigation curtailments using remote sensing and streamflow gages

Klamath Tribal Water Quality Consortium | September 11th, 2023

Key Points • Satellite remote sensing data indicated that curtailment orders in 2022 reduced consumptive water use (evapotranspiration, ETa) on agricultural lands i

Key Points • Satellite remote sensing data indicated that curtailment orders in 2022 reduced consumptive water use (evapotranspiration, ETa) on agricultural lands in Shasta Valley, but not Scott Valley. • Streamflow gage data indicate that flows in the Shasta River and some Scott River tributaries (Shackleford and French creeks) were substantially higher in summer 2022 than 2020 or 2021, but similar increases did not occur in the mainstem Scott River. • A likely major reason for the lack of Scott River flow increases was that groundwater use was allowed to continue under Local Cooperative Solutions (LCS) agreements in which water users agreed to reduce pumping by 30% from a prior year baseline. Despite abundant worldwide evidence that reducing consumptive use (i.e., evapotranspiration) is key to increasing environmental water, all LCS cropping and irrigation practices were given equal weight toward the 30% reduction, regardless of the effects on consumptive use. Pumping was not measured and compliance was primarily self-reported, with limited independent verification.