Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

PLOS | February 24th, 2021

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the pa

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed.

Record of Decision, Trump Administration Action 5 Operations Plan for the Central Valley and State Water Projects, per Executive Order 14181

U.S. Bureau of Reclamation (USBR) | December 4th, 2025

On January 24, 2025, President Donald J. Trump issued Executive Order 14181 “Emergency Measures To Provide Water Resources In California And Improve Disaster Response I

On January 24, 2025, President Donald J. Trump issued Executive Order 14181 “Emergency Measures To Provide Water Resources In California And Improve Disaster Response In Certain Areas.” A Presidential Memorandum titled “Putting People Over Fish” was signed four days before the Executive Order and references a reliable water supply, but the specific direction to the CVP is found in Executive Order 14181. Section 2 of Executive Order 14181 requires, among other measures, (c) The Secretary of the Interior, including through the Bureau of Reclamation, shall utilize his discretion to operate the CVP to deliver more water and produce additional hydropower, including by increasing storage and conveyance, and jointly operating federal and state facilities, to high­need communities, notwithstanding any contrary State or local laws. The Bureau of Reclamation shall take all available measures to ensure that State agencies — including the California Department of Water Resources — do not interfere with the Bureau of Reclamation’s operation of the project to maximize water delivery to high­need communities or otherwise, including but not limited to the issuance of a new Record of Decision maximizing water deliveries and consistent with the 2020 Record of Decision. Subsection (g) calls for a “proposed plan, for review by the Secretaries, to appropriately suspend, revise, or rescind any regulations or procedures that unduly burden such projects and are not necessary to protect the public interest or otherwise comply with the law.” This ROD implements initial actions in response to Executive Order 14181. Click here for the Reclamation Long Term Operations page,  here for response to the Trump Action 5 gambit from California Department of Water Resources, and here for the response from the State Water Resources Control Board

Recovery plan for Central Valley winter-run chinook salmon, spring-run chinook salmon, and steelhead

National Marine Fisheries Service (NMFS) | July 7th, 2014

Recovery is the process by which listed species and their ecosystems are restored and their future is safeguarded to the point that protections under the Endangered Speci

Recovery is the process by which listed species and their ecosystems are restored and their future is safeguarded to the point that protections under the Endangered Species Act (ESA) are no longer needed. The goal of this Recovery Plan is to recover the endangered Sacramento River winter-run Chinook salmon Evolutionarily Significant Unit (ESU), the threatened Central Valley spring-run Chinook salmon ESU, and the threatened California Central Valley steelhead Distinct Population Segment (DPS). Recovering these species and the Central Valley, San Francisco Bay-Delta Estuary, and Pacific Ocean ecosystems that support them will be challenging and will require shifts in societal values. Californians must work together towards a conservation ethic and practice that ensures wild salmon and steelhead are an important part of coastal California and Central Valley culture for many generations to come.

Recovery Plan for Sacramento-San Joaquin Delta native fishes

U.S. Fish and Wildlife Service (FWS) | November 26th, 1996

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splitta

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splittail (splittail) was proposed as a threatened species on January 6, 1994. This recovery plan will recommend restoration criteria for the splittail that would be appropriate recovery criteria should the species be listed. Longfin smelt, green sturgeon, spring-run, late fall-run, and San Joaquin fall-run chinook salmon are species of concern for which restoration criteria are recommended. Information is also included on Sacramento perch, a species believed to be extirpated from the Delta at this time. Habitat Requirements and Limiting Factors: The eight species included in this recovery plan depend on the Sacramento-San Joaquin Delta for a significant segment of their life history. Threats to the Delta ecosystem and these species include loss of habitat due to increased freshwater exports resulting in increased salinity, loss of shallow-water habitat due to dredging, diking and filling, introduced aquatic species that have disrupted the food chain, and entrainment (movement offish by currents produced by diversions) in State, Federal and private water diversion. State and Federal water projects have also changed the pattern and timing of flows through the Delta. The salmon races are affected by sport and commercial harvest as well as by interactions with hatchery stocks. Recovery and Restoration Objective: Delisting of delta smelt. Restoration of splittail, longfin smelt, green sturgeon, spring-run, late fall-run, San Joaquin fall-run chinook salmon, and Sacramento perch. Recovery and Restoration Criteria: Recovery criteria are quantifiable and species specific and can be used to (1) monitor effectiveness of recovery actions, (2) determine when a species has recovered to a secure level (stabilized), and (3) determine when a species qualifies for delisting. In many cases, criteria are based on two independent measures: population abundance and geographic distribution. For each species a historic base period was established using available data to characterize abundance and distribution during a pre-decline period. The time period over which abundance and distribution criteria must be met was set at five generations. For five of the eight species there is an additional requirement of meeting the criteria through a minimum number of years of stressful environmental conditions. Action Needed: 1. Enhance and restore aquatic and wetland habitat in the Sacramento-San Joaquin River estuary. 2. Reduce effects of commercial and recreational harvest. 3. Reduce effects of introduced aquatic species on Delta native fishes. 4. Change and improve enforcement ofregulatory mechanisms. 5. Conduct monitoring and research on fish biology and management requirements. 6. Assess recovery management actions and re-assess prioritization of actions. 7. Increase public awareness of importance of Delta native fishes.

Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds

San Francisco Estuary Institute (SFEI) | April 8th, 2014

San Francisco Bay (California, USA) and its local watersheds present an interesting case study in estuarine mercury (Hg) contamination. This review focuses on the most pr

San Francisco Bay (California, USA) and its local watersheds present an interesting case study in estuarine mercury (Hg) contamination. This review focuses on the most promising avenues for attempting to reduce methylmercury (MeHg) contamination in Bay Area aquatic food webs and identifying the scientific information that is most urgently needed to support these efforts.

Regional Monitoring Program (RMP) for Water Quality in San Francisco Bay, 2020 Detailed Workplan and Budget

San Francisco Estuary Institute (SFEI) | December 1st, 2019

Regional Monitoring Program for Water Quality in San Francisco Bay 2016 Detailed Workplan and Budget

San Francisco Estuary Institute (SFEI) | November 10th, 2015

In 2016 the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is entering its 24th year of collecting data and communicating information to suppor

In 2016 the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is entering its 24th year of collecting data and communicating information to support water quality management decisions. This Detailed Workplan and Budget describes the activities that will be completed in 2016 and their proposed funding levels.

Regional patterns in hydrologic response, a new three-component metric for hydrograph analysis and implications for ecohydrology, Northwest Volcanic Aquifer Study Area, USA

Journal of Hydrology (Elsevier) | June 12th, 2020

Spatial patterns of hydrologic response were examined for the Northwest Volcanic Aquifer Study Area (NVASA). The utility of established hydrograph-separation methods for

Spatial patterns of hydrologic response were examined for the Northwest Volcanic Aquifer Study Area (NVASA). The utility of established hydrograph-separation methods for assessing hydrologic response in permeable volcanic terranes was assessed and a new three-component metric for hydrograph analysis was developed. The new metric, which partitions streamflow into subcomponents defined by the timescales of hydrologic response (e.g., fast-runoff, intermediate-interflow and slow-baseflow), was used to gain a fundamental understanding of the regional hydrology, investigate sub-regional differences, influencing factors, and ecohydrological implications. The combined effects of NVASA’s physiography, climate and geology create a strongly coupled surface-groundwater system that produces copious baseflow and limited quantities of runoff and interflow. Patterns of hydrologic response are influenced by the type and rate of precipitation and permeability of the underlying geology. Under variable precipitation conditions the hydrologic response of volcanic terranes with similar permeability and subsurface-storage capacity can be significantly different. From a water management and ecohydrology perspective, understanding regional patterns of hydrologic response and sub-regional differences is fundamental. Results indicate that minimum-flow methods provide the most conservative estimate of baseflow and may be the most robust for filtering out snowmelt bias in baseflow estimates. Baseflow contributes ∼75% of the perennial streamflow across the NVASA and represents a critical component of the regional water supply that provides critical cold-water habitat.

Relationship between wetland condition, stress, and buffer

San Francisco Estuary Institute (SFEI) | April 25th, 2016

Relationship between wetland size and CRAM condition scores for depressional wetlands

San Francisco Estuary Institute (SFEI) | March 28th, 2016