Effect of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 15th, 2018

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary ro

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary rock-fill barriers constructed in waterways located in the southern portion of the Sacramento-San Joaquin Delta (Delta) near the cities of Tracy and Lathrop in San Joaquin County, California (Figure 1-1). Three of the temporary barriers—Old River at Tracy (ORTB), Middle River (MRB), and Grant Line Canal (GLCB), collectively, the south Delta agricultural barriers (SDABs)—are constructed and operated during the agricultural irrigation season, usually April through November. The SDABs are designed to act as flow control structures, retaining tidal fresh water behind each barrier following a flood tide. The fourth barrier, Head of Old River Barrier (HORB), is installed during the spring and fall as a fish guidance barrier. The HORB is normally installed in the spring to prevent juvenile fall-run San Joaquin River Chinook Salmon (Oncorhynchus tshawytscha) and juvenile Central Valley steelhead (Oncorhynchus mykiss) 2 from emigrating through Old River toward the south Delta water export facilities at the intakes of the State Water Project (SWP) and federal Central Valley Project (CVP). In the fall, the HORB helps to guide adult San Joaquin River Chinook Salmon to spawning locations in the upper watershed. Installation, operation, and removal of the SDABs has the potential to harm, harass, or cause mortality to fish species of management concern to the National Marine Fisheries Service (NMFS), specifically, juvenile fall-run Chinook Salmon which are NMFS Species of Concern (NMFS 2010), juvenile Central Valley steelhead which is a threatened species, an Endangered Species Act (ESA) Section 10j experimental population (63 Federal Register [FR] 13347), and juvenile Green Sturgeon (Acipenser medirostris), also a federally listed threatened species (71 FR 17757). The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009).

Effects Analysis for the Delta Smelt Fall Habitat Action in 2019

U.S. Bureau of Reclamation (USBR) | August 1st, 2019

Effects of Groundwater Pumping on Agricultural Drains in the Tule Lake Subbasin, Oregon and California

U.S. Geological Survey (USGS) | July 24th, 2015

Since 2001, irrigators in the upper Klamath Basin have increasingly turned to groundwater to compensate for reductions in surface-water allocation caused by shifts from

Since 2001, irrigators in the upper Klamath Basin have increasingly turned to groundwater to compensate for reductions in surface-water allocation caused by shifts from irrigation use to instream flows for Endangered Species Act listed fishes. The largest increase in groundwater pumping has been in and around the Bureau of Reclamation’s Klamath Irrigation Project, which includes the Tule Lake subbasin in the southern part of the upper Klamath Basin. Agricultural drains on the Klamath Project are an important source of water for downstream irrigators and for the Tule Lake and Lower Klamath Lake National Wildlife Refuges. U.S. Geological Survey regional groundwater-flow model simulations and records of irrigation-return flow pumped from the Tule Lake subbasin into the adjacent Lower Klamath Lake subbasin have indicated that water-level declines from pumping may be causing decreased flow of shallow groundwater to agricultural drains. To better define the effect of increased pumping on drain flow and on the water balance of the groundwater system, the annual water volume pumped from drains in three subareas of the Tule Lake subbasin was estimated and a fine-grid, local groundwater model of the Tule Lake subbasin was constructed. Results of the agricultural-drain flow analysis indicate that groundwater discharge to drains has decreased such that flows in 2012 were approximately 32,400 acre-ft less than the 1997–2000 average flow. This decrease was concentrated in the northern and southeastern parts of the subbasin, which corresponds with the areas of greatest groundwater pumping. Model simulation results of the Tule Lake subbasin groundwater model indicate that increased supplemental pumping is the dominant stress to the groundwater system in the subbasin. Simulated supplemental pumping and decreased recharge from irrigation between 2000 and 2010 totaled 323,573 acre-ft, 234,800 acre-ft (73 percent) of which was from supplemental pumping. The response of the groundwater system to this change in stress included about 180,500 acre-ft (56 percent) of decreased groundwater discharge to drains and a 126,000 acre-ft (39 percent) reduction in aquifer storage. The remaining 5 percent came from reduced groundwater flow to other model boundaries, including the Lost River, the Tule Lake sumps, and interbasin flow.

Effects of Hydraulic Conditions on Salvage Efficiency of Adult Delta Smelt at the Tracy Fish Collection Facility

U.S. Bureau of Reclamation (USBR) | February 29th, 2016

Effects of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 28th, 2018

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS BiOps, a study of the effects of the three SDABs (i.e., ORTB, MRB, and GLCB) on emigrating (i.e., out-migrating) juvenile salmonids was conducted (2010–2011) and the results are reported in this document. There were four effects considered in this study: 1) survival of juvenile salmonids (Ŝ); 2) juvenile salmonid time-in-vicinity (TIV) of a barrier; 3) predation on juvenile salmonids; and 4) predatory fish density evaluations near the barriers before-, during-, and after- construction during each study year. For one barrier, the ORTB, two-dimensional (2D) acoustic fish tracks for juvenile salmonids were used to evaluate: 1) the rates of successful passage through the barrier; and 2) route selection through the barrier. In addition, utilizing the ORTB 2D fish tracks for both juvenile salmonids and predatory fish, a mixture model (Romine et al. 2014) approach was employed to determine the probability that a juvenile salmonid had been eaten by a predatory fish in the vicinity of the ORTB.

Empirical and Experimental Analyses of Secondary Louver Efficiency at the Tracy Fish Collection Facility: March 1996 to November 1997

U.S. Bureau of Reclamation (USBR) | January 30th, 2004

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 and Threatened Wildlife and Plants; Endangered Species Act Compensatory Mitigation Policy

Federal Register | December 27th, 2016

SUMMARY: We, the U.S. Fish and Wildlife Service (Service or USFWS), announce the final Endangered Species Act (ESA) Compensatory Mitigation Policy. The new policy steps d

SUMMARY: We, the U.S. Fish and Wildlife Service (Service or USFWS), announce the final Endangered Species Act (ESA) Compensatory Mitigation Policy. The new policy steps down and implements recent Executive Office, Department of the Interior, and Service mitigation policies that reflect a shift from project-by-project to landscape-scale approaches to planning and implementing compensatory mitigation. The new policy is established to improve consistency and effectiveness in the use of compensatory mitigation as recommended or required under the ESA. The ESA Compensatory Mitigation Policy covers permittee-responsible mitigation, conservation banking, in-lieu fee programs, and other third-party mitigation mechanisms, and stresses the need to hold all compensatory mitigation mechanisms to equivalent and effective standards. DATES: This policy is effective on December 27, 2016.

Endangered Species Act (ESA): The Exemption Process

Congressional Research Service (CRS) | January 27th, 2017

The Endangered Species Act (ESA) is designed to protect species from extinction, but it includes an exemption process for those unusual cases where the public benefit fro

The Endangered Species Act (ESA) is designed to protect species from extinction, but it includes an exemption process for those unusual cases where the public benefit from an action is determined to outweigh the harm to the species. This process was created by a 1978 amendment to the ESA, but it is rarely used. This report will discuss the exemption process for an agency action, with examples from past controversies, and its potential for application to actions that may affect current controversies, such as water supply. The ESA mandates listing and protecting species that are endangered or threatened with extinction. Listing a species limits activities that could affect that species and provides penalties for taking individuals of that species. The ESA also requires federal agencies to consult with the Fish and Wildlife Service or the National Marine Fisheries Service (together, the Services) to determine whether a federal action may jeopardize the continued existence of a species or harm its critical habitat. The consultation process may lead to an opinion by one of the Services that the action will jeopardize listed species or harm their critical habitats unless certain reasonable and prudent alternatives are included in the action. Rarely, the federal action agency may hold that those alternatives are inconsistent with the agency action. In other extremely rare cases, the Services may find that no alternatives are available that would allow the project to proceed and still prevent jeopardy. In either case, the following are the categories of potential applicants that can apply for an exemption for a federal action despite its effects on listed species or their critical habitat: the federal action agency interested in proceeding with the action, an applicant for a federal license or permit whose application was denied primarily because of the prohibitions of ESA requiring that federal agency actions avoid jeopardy to threatened or endangered species or harm to their critical habitats, or the governor of the state where the action was to have occurred. An exemption application is considered by a specially convened committee which may exempt the federal agency’s action from the prohibitions of the ESA. The exemption process allows major economic factors to be judged to outweigh the ESA’s mandate to recover a species when the federal action is found to be in the public interest and is nationally or regionally significant. The exemption process has been invoked with a dam on the Tellico River (TN), a water project in the Platt River (WY and NE), and timber sales (OR). In three other instances, the process was begun but was aborted before a decision was reached. In addition, there has been interest over the years in invoking the process in light of controversies over management of federal and state water resource projects in California, although no application has ever been filed. When a project achieves such levels of controversy, Congress is sometimes asked to intervene in the outcome, as it did in the case of the Tellico Dam and an endangered fish in the late 1970s.