Independent Review Panel (IRP) Report for the 2015 Long-Term Operations Biological Opinions (LOBO) Annual Science Review

Delta Stewardship Council (Delta Council) | December 1st, 2015

This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (N

This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (NMFS) and the U.S. Fish & Wildlife Service (USFWS) as to the efficacy of water operations and certain regulatory actions prescribed by their respective Long-term Operations Biological Opinions’ (LOBO) Reasonable and Prudent Alternative Actions (RPAs) as applied from October 1, 2014 through September 30, 2015 (Water Year 2015).  This year’s annual review focused primarily on: (1) Shasta Reservoir and Sacramento River temperature monitoring, modeling, and management, (2) the River Assessment for Forecasting Temperature (RAFT) decision support tool (model), (3) an Enhanced Particle Tracking Model (E-PTM), and (4) a USFWS report on past, present, and future approaches to incidental take of Delta Smelt.  After reviewing a required set of written documents (Appendix 1), the IRP convened at a public workshop in Sacramento, CA on 5-6 November 2015. The first day of the 2-day workshop included agency presentations and provided a forum for the IRP to interact and consider information presented on water operations, temperature modeling, monitoring and RPA Actions as implemented in yet another critically dry 2015 water year. On the second day, the IRP deliberated in a private session beginning at 9:00 a.m. in order to prepare and present their initial findings at the public workshop at 2:00 p.m., after which there was an opportunity for agency representatives, members of the public, and the IRP members to comment and otherwise exchange impressions and information. Subsequent IRP communication and deliberations were conducted via email and conference calls in the course of drafting this final report. Click here for federal agency response letter

Independent Review Panel (IRP) Report for the 2017 Long-term Operations Biological Opinions (LOBO) Biennial Science Review (January 24, 2018)

Delta Stewardship Council (Delta Council) | January 31st, 2018

Initial Alternatives Information Report for the North/Central Delta Improvement Study (Delta Cross Channel, Franks Tract, and Through- Delta Facility Evaluation)

U.S. Bureau of Reclamation (USBR) | March 17th, 2010

The U.S. Department of the Interior (Interior) Bureau of Reclamation (Reclamation) and the California Department of Water Resources (DWR) are evaluating the feasibility o

The U.S. Department of the Interior (Interior) Bureau of Reclamation (Reclamation) and the California Department of Water Resources (DWR) are evaluating the feasibility of using conveyance and operations actions in the north and central region of the Sacramento–San Joaquin River Delta (Delta) to improve water quality and fish conditions. Specifically, Reclamation is evaluating the feasibility of these actions in the North/Central Delta Improvement Study (NoCDIS or Study). The Initial Alternatives Information Report (IAIR) identifies, discusses, and screens measures to address the problems and opportunities. These measures are used to develop initial alternatives. Initial alternatives from the IAIR will be incorporated into and refined in the subsequent Plan Formulation Report (PFR). Subject to continued appropriations and a determination of federal interest, the Study should culminate in an Environmental Impact Statement/Environmental Impact Report (EIS/EIR) and a Feasibility Report. Reclamation is the federal lead agency for National Environmental Policy Act (NEPA) compliance, and DWR is the state lead agency for California Environmental Quality Act (CEQA) compliance.

Interagency Fish Passage Steering Committee 2014 Annual Report Focusing on the Shasta Dam Fish Passage Evaluation

Delta Stewardship Council (Delta Council) | July 1st, 2014

Interim instream flow criteria for the protection of fishery resources in the Scott River watershed, Siskiyou County

California Department of Fish and Wildlife (CDFW) | February 6th, 2017

This document describes the methods and results of an analysis using historical flow data and regional regression relationships to develop interim instream flow criteria

This document describes the methods and results of an analysis using historical flow data and regional regression relationships to develop interim instream flow criteria suitable for anadromous fish in the Scott River watershed in Siskiyou County. The Scott River watershed provides aquatic habitat for four species of anadromous fish; Chinook Salmon (Oncorhynchus tshawytscha), Coho Salmon (O. kisutch), steelhead trout (O. mykiss), and Pacific Lamprey (Lampetra tridentata). Specifically, the Scott River is one of the most important Coho Salmon spawning and rearing tributaries in the Klamath River watershed. Instream flow requirements can be generated from flow standard setting techniques or from the results of site specific studies. The interim instream flow criteria presented for the Scott River were developed using flow standard setting techniques. Stream flow standards derived from standard setting techniques are designed to identify the environmental resource in need of flow protection, identify biologically significant criterion that can be used to measure potential flow related impacts, and specify the amount of flow required to protect the resource. Most individual standards evaluate only one or more, but not all the criterion needed to fully evaluate the flow needs of an aquatic species. This limitation can lead to prescribing a single minimum threshold or “flat-line” affect (Poff et al. 1997). The seasonal and inter-annual variability in the hydrograph must be maintained to protect stream ecology and provide an ecosystem based standard (Annear 2004). To account for the seasonal and the inter-annual hydrologic variability of the Scott River, the Department applied a detailed hydrologic analysis along with application of three standard setting methods to evaluate the life history flow needs of salmonids in the Scott River near Fort Jones. Adult fish passage was estimated using the equation developed by R2 Resources (R2 2008) for the State Water Resources Control Board’s (SWRCB) North Coast Instream Flow Policy (SWRCB 2014), spawning and juvenile rearing were evaluated using the Hatfield and Bruce regional equations (Hatfield and Bruce 2000), and the results were adjusted monthly based on estimates of unimpaired hydrology using Tessmann’s adaptation (Tessmann 1980) of the Tennant or Montana Method (Tennant 1975).

Issue Paper for the San Joaquin River spring-run Chinook experimental population – Delta impacts

National Marine Fisheries Service (NMFS) | July 23rd, 2013

Juvenile Production Estimate (JPE) Calculation and Use/Application of Survival Data from Acoustically-tagged Chinook Salmon Releases Report

Delta Stewardship Council (Delta Council) | February 21st, 2014

Each year, NOAA’s National Marine Fisheries Service (NMFS) estimates the number of juvenile winter-run Chinook salmon expected to enter the Delta. NMFS’ June 4, 2009

Each year, NOAA’s National Marine Fisheries Service (NMFS) estimates the number of juvenile winter-run Chinook salmon expected to enter the Delta. NMFS’ June 4, 2009, biological and conference opinion on the long-term operation of the Central Valley Project and State Water Project provides an incidental take limit on natural juvenile winter-run based on the juvenile production estimate.

Juvenile salmonids traverse coastal meta-nurseries that connect rivers via the sea

Ecological Society of America (ESA) | April 30th, 2025

Conventionally, juvenile salmonids are thought to migrate unidirectionally from freshwater systems to marine systems and therefore only inhabit natal drainages. Although

Conventionally, juvenile salmonids are thought to migrate unidirectionally from freshwater systems to marine systems and therefore only inhabit natal drainages. Although scattered evidence suggests juveniles can move bidirectionally between freshwater rivers and the ocean, including into non-natal drainages, such movements have never been documented with high replication. Here, we detected hundreds of movements of juvenile salmonids between drainages that involved 0–22% of cohort emigrants in Washington State and California. Individuals moved up to nine times and between drainages up to 70 km apart. These findings reveal a life-history type of salmonids whose remarkably complex migrations have gone unnoticed. Implicitly, juveniles may use any coastal freshwater habitat accessible from the sea and may not descend from spawning populations of drainages they inhabit. Consequently, typical conservation focused on natal drainages may overlook freshwater habitat elsewhere. A concept of coastal areas as meta-nurseries formed by multiple watersheds connected by the sea may accurately describe anadromous species’ habitat options and better inform management.

Klamath Basin Settlement Agreements

Congressional Research Service (CRS) | October 21st, 2015

The Klamath River Basin on the California-Oregon border is a focal point for local and national discussions on water allocation and species protection. Previously, water

The Klamath River Basin on the California-Oregon border is a focal point for local and national discussions on water allocation and species protection. Previously, water and species management issues have exacerbated competition and generated conflict among several interests—farmers; Indian tribes; commercial and sport fishermen; federal water project and wildlife refuge managers; environmental groups; hydropower facility operators; and state, local, and tribal governments. Drought conditions and a call for water by senior water rights holders in 2013 have again brought these issues to the forefront. In 2010, the Secretary of the Interior and the governors of Oregon and California, along with multiple interest groups, announced the results of a multiyear negotiation process to resolve long-standing issues in the basin: two interrelated agreements, supported by the federal government and signed by the two states and numerous other parties. These agreements, known as the Klamath Basin Restoration Agreement (KBRA) and the Klamath Hydroelectric Settlement Agreement (KHSA), together aim to provide for water deliveries to irrigators and wildlife refuges, fish habitat restoration, and numerous other related actions. Generally, the KBRA provides for actions intended to restore Klamath fisheries and for assurances for water deliveries to wildlife refuges and federal project irrigators under certain circumstances, among other things. The KHSA lays out a process that could lead to the removal of four privately owned dams on the Klamath River. This dam removal would be one of the largest and most complex projects of its kind ever undertaken. Some parts of the Klamath agreements are being carried out under existing authorities. Studies to inform a determination on dam removal under the KHSA by the Secretary of the Interior are complete, and some restoration actions have been initiated. However, congressional authorization is required for the most significant components of the agreements to be implemented. The KBRA and KHSA did not address all outstanding issues in the basin. A water rights adjudication by the state of Oregon (in progress since the 1970s) is ongoing. In 2013, the adjudication reaffirmed “time immemorial” tribal water rights in the upper part of the Klamath Basin, confirming that tribal water rights are senior to those of other water rights holders. This resulted in a “call” on water rights (i.e., notice by senior water rights holders that their demands exceed available flows), and led to reductions to water supplies for some junior users during the low water year of 2013. To resolve these issues and prevent such a scenario from occurring again, a separate settlement agreement (the Upper Klamath Basin Settlement Agreement) was negotiated by stakeholders and finalized in April 2014. To be implemented, the agreement would need to be authorized along with the KBRA and KHSA. The KBRA and KHSA were originally set to expire in 2012 if no authorizing legislation was enacted, but they have since been extended (most recently through 2015). Parties may also withdraw individually from the agreements, and several parties initiated this process of withdrawal. In the 114th Congress, S. 133 would authorize the Klamath agreements, including a suite of new federal actions that have received support from disparate parties and are required for the agreements to be implemented. Previous legislation in the 113th Congress (S. 2379) was ordered to be reported out of the Senate Committee on Energy and Natural Resources on November 13, 2014.

Klamath River Basin Issues: An Overview of Water Use Conflicts

Congressional Research Service (CRS) | June 13th, 2002

Severe drought in 2001 affected the Klamath River Basin, an area on the California-Oregon border, exacerbating competition for scarce water resources and generating confl

Severe drought in 2001 affected the Klamath River Basin, an area on the California-Oregon border, exacerbating competition for scarce water resources and generating conflict among several interests – farmers, municipal and industrial users, commercial and sport fishermen, other recreationists, federal wildlife refuges, environmental groups, and Indian Tribes. The conflicts over water distribution and allocation are physically and legally complex, reflecting the varied and sometimes competing uses of limited water supplies in the Upper Basin. On April 6, 2001, the Bureau of Reclamation (Bureau), which has supplied water to farms in the Upper Basin for nearly 100 years, announced that “no water [would] be available” for farms normally receiving water from the Upper Klamath Lake, so that scarce water could be used to protect species listed as endangered or threatened under the Endangered Species Act (ESA). Water was available to some farmers from other sources (e.g., wells and other Bureau sources); however, many farmers were not able to plant or harvest crops due to severe cutbacks in water supplies. Emotions ran high on all sides of the issues, and the water control gates were unlawfully opened by protesters. Although the Basin has received significantly more precipitation in 2002, many issues remain in dispute. In addition, several judicial decisions have affected the issues with respect to the listed species as well as tribal rights. On May 31, 2002, the U.S. Fish and Wildlife Service and the National Marine Fisheries Service both issued Final Biological Opinions on the Bureau’s 10-year Operation Plan for the Klamath Project. The agencies found that the Bureau’s proposed action is likely to jeopardize the continued existence of the two listed suckers and coho salmon, as well as result in the adverse modification of proposed critical habitat; however, both Opinions also included “reasonable and prudent alternatives” for operating the Project that would remove the jeopardizing effects of the proposed action. However, on June 3, 2002, the Bureau formally rejected both Final Biological Opinions, but opted instead to operate under a one-year plan that it asserts complies with the Opinions. Independently, in March 2002, the President appointed a high-level working group to develop solutions. Congress has responded to the controversy in a number of ways, including holding several oversight hearings and appropriating funds for water conservation activities in the area. This report provides background on the geographic, historic, and legal underpinnings of the current conflicts. Because the report focuses on the current conflicts, it deals primarily with Klamath Project operations in the Upper Klamath Basin and effects associated with water releases from Upper Klamath Lake.