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

Environmental Law Foundation, et al. Petitioners, v. State Water Resources Control Board, et al. Respondents

State of California | July 15th, 2014

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.

Environmental Water Account: Need for Legislative Definition and Oversight

Legislative Analyst's Office (LAO) | January 29th, 2001

We recommend that the Legislature hold oversight hearings to evaluate CALFED's proposal for the Environmental Water Account, implemented to acquire water for endangered s

We recommend that the Legislature hold oversight hearings to evaluate CALFED's proposal for the Environmental Water Account, implemented to acquire water for endangered species protection and recovery in the Bay-Delta region. There are many policy and implementation issues that the Legislature should consider before CALFED proceeds with the new program, including the program's costs, benefits, impacts, governance, and funding. Funding should be governed by the "beneficiary pays" principle.

Envisioning Futures for the Sacramento-San Joaquin Delta

Public Policy Institute of California (PPIC) | January 25th, 2007

California’s Sacramento-San Joaquin Delta is widely perceived to be in crisis today: its levee system is fragile, many of its native species are declining rapidly, and

California’s Sacramento-San Joaquin Delta is widely perceived to be in crisis today: its levee system is fragile, many of its native species are declining rapidly, and it lacks strong governing institutions to deal with its problems. In its current state, the Delta is unsustainable for almost all stakeholders. This report provides a comprehensive, scientifically up-to-date analysis and outlines several alternative management strategies for the Delta.

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.

Estimating Exposure of Piscivorous Birds and Sport Fish to Mercury in California Lakes Using Prey Fish Monitoring—A Predictive Tool for Managers

U.S. Geological Survey (USGS) | May 22nd, 2015

Numerous water bodies in California are listed under the Clean Water Act as being impaired due to mercury (Hg) contamination. The Surface Water Ambient Monitoring Program

Numerous water bodies in California are listed under the Clean Water Act as being impaired due to mercury (Hg) contamination. The Surface Water Ambient Monitoring Program (SWAMP), via the Bioaccumulation Oversight Group (BOG), has recently completed statewide surveys of contaminants in sport fish tissue from more than 250 lakes and rivers in California and throughout coastal waters. This effort focused on human health issues but did not include beneficial uses by wildlife. Many piscivorous birds such as grebes, terns, cormorants, and mergansers eat fish smaller than those that were sampled by BOG, and sport fish Hg concentrations are not always indicative of wildlife exposure to Hg; therefore, the BOG surveys could not address whether wildlife were at risk due to Hg-induced reproductive impairment in these lakes. We used western grebes (Aechmophorus occidentalis) and Clark’s grebes (Aechmophorus clarkii) as our index of wildlife exposure to Hg in California lakes. Grebes are widely distributed in lakes throughout California and, as piscivorous waterbirds, are near the top of the food chain in lakes. Additionally, grebes become flightless after they arrive at their summer locations. Thus, grebes are useful representatives for wildlife risk from local, lake-specific contaminant exposure. Grebes also breed at many lakes throughout California, making them susceptible to impaired reproduction due to local Hg contamination. We developed a tool for estimating wildlife and sport fish risk from Hg exposure based on Hg concentrations in prey fish. This quantitative tool can be used to predict Hg concentrations in grebe blood, grebe eggs, and sport fish, thus facilitating a feasible alternative for adequately estimating wildlife exposure when more comprehensive wildlife sampling is not possible. Specifically, we sampled grebes, prey fish, and sport fish simultaneously at 25 lakes throughout California during the spring and summer of 2012 and 2013 when breeding birds are particularly vulnerable to Hg-induced reproductive impairment. We selected lakes based on a combination of factors, including lakes from southern and northern California, of various sizes, shapes, and elevations, with a range of sport fish Hg exposure levels where largemouth bass (Micropterus salmoides) was the primary sport fish, and with a history of use by grebes. Using these factors ensured that our results are representative of a broad range of lakes and reservoirs in California and are comparable to prior BOG studies. Specifically, we addressed three management questions: Does methylmercury pose significant risks to aquatic life in a representative sample of California lakes and reservoirs? Can a correlational approach be applied on a statewide basis to estimate risks to birds? What are appropriate water-quality monitoring requirements to address methylmercury exposure in wildlife?

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.

Estuary News, April 1993

Publisher not available | April 15th, 1993