Flooded Wetland Availability for Breeding Waterfowl in a Mediterranean Climate: Mapping 38 Years of Historical Data in Suisun Marsh, California

University of California, Davis (UC Davis) | December 19th, 2025

Most managed wetlands in California are ephemeral and are purposefully flooded during the fall and winter for over-wintering waterfowl and are dry during the spring and s

Most managed wetlands in California are ephemeral and are purposefully flooded during the fall and winter for over-wintering waterfowl and are dry during the spring and summer waterfowl breeding season. Only semi-permanent and permanent wetlands remain flooded through the critical summer brood-rearing period for ducklings. We examined flooded wetland availability for breeding waterfowl in the brackish Suisun Marsh (California, USA) annually during the spring (April 27–May 17, during peak nesting) and summer (June 17–July 7, during peak duckling brood rearing), for a 38-year period using Landsat satellite imagery and spectral mixture analysis. Flooded wetland area increased 43% in spring and 48% in summer from 1984 to 2021 but varied among years (spring: 37.6–88.6 km2; summer: 17.7–57.5 km2). This increase in flooded wetland area over the past four decades was due to just a few sites, with only 24% (spring) and 15% (summer) of the 198 land-owner parcels increasing in flooded area. Flooded wetland area in the spring was unrelated to annual precipitation between October and April (range: 25–104 cm) or spring precipitation between January and April (range: 8-65 cm), whereas flooded wetland area in the summer was weakly correlated to both annual and spring precipitation. Flooded wetland area in spring and summer was also weakly correlated with the median daily outflow from the Sacramento-San Joaquin River Delta between March 15 and June 15, which corresponds to a critical period of wetland water management for breeding waterfowl. Our results indicate that spring and summer flooded wetland habitat for breeding waterfowl has slightly increased over the past four decades, varies annually, and is mostly dependent on local wetland management practices rather than on precipitation or Delta outflows. Managing habitats as semi-permanent wetlands would increase flooded wetland habitat in the spring and summer and provide habitat for nesting hens and ducklings.

Floodplain farm fields provide novel rearing habitat for Chinook salmon

PLOS | June 7th, 2016

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and f

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and floodplain wetlands drained for flood control and agriculture. In the Central Valley of California, USA, where less than 5% of floodplain wetland habitats remain, a critical conservation question is how can farmland occupying the historical floodplains be better managed to improve benefits for native fish and wildlife. In this study fields on the Sacramento River floodplain were intentionally flooded after the autumn rice harvest to determine if they could provide shallow-water rearing habitat for Sacramento River fall-run Chinook salmon (Oncorhynchus tshawytscha). Approximately 10,000 juvenile fish (ca. 48 mm, 1.1 g) were reared on two hectares for six weeks (Feb-March) between the fall harvest and spring planting. A subsample of the fish were uniquely tagged to allow tracking of individual growth rates (average 0.76 mm/day) which were among the highest recorded in fresh water in California. Zooplankton sampled from the water column of the fields were compared to fish stomach contents. The primary prey was zooplankton in the order Cladocera, commonly called water fleas. The compatibility, on the same farm fields, of summer crop production and native fish habitat during winter demonstrates that land management combining agriculture with conservation ecology may benefit recovery of native fish species, such as endangered Chinook salmon.

Flow Recommendations to the State Water Resources Control Board

California Department of Fish and Wildlife (CDFW) | May 22nd, 2008

Pursuant to Public Resouces Code (PRC) Section 10001, in the early 1980s, the Department of Fish and Game (DFG) in coordination with all regional DFG offices, identified

Pursuant to Public Resouces Code (PRC) Section 10001, in the early 1980s, the Department of Fish and Game (DFG) in coordination with all regional DFG offices, identified 21 streams and watercourses for which minimum flow levels needed to be established in order to assure the continued viability of stream-related fish and wildlife resources. Over approximately 20 years, DFG investigated the instream flow needs of these listed streams and watercourses.  The investigations included field studies, data analyses, and consultations with local, state, and federal agencies and interested individuals and organizations.  As a result of the investigations, DFG prepared instream flow recommendations for the listed streams. The attached transmittal summarizes the flow recommendations prepared by DFG pursuant to PRC 10000.  Submission of these recommendations to the State Water Resources Control Board (SWRCB) complies with PRC Section 10002. As will be evident upon review, the attached flow recommendations are intended to supplement, but not replace, current administrative records.  The attached flow recommendations should not be implemented by the SWRCB without further investigation and consideration of supporting information that would identify constraints or limitations that qualify each recommendation. In addition, as noted on each recommendation, some studies were done many years ago using early methods.  DFG has established an administrative file in the Water Branch that contains the resource documents cited in the flow recommendations.

Flows and Fishes in the Sacramento-San Joaquin Delta

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

Record-low counts of Delta smelt at a time of persistent drought underscore the importance and challenges of managing freshwater flows for the benefit of fishes in the Sa

Record-low counts of Delta smelt at a time of persistent drought underscore the importance and challenges of managing freshwater flows for the benefit of fishes in the Sacramento-San Joaquin Delta while also meeting human demands for water. Understanding the effects of water flows on fishes is central to understanding how the Delta ecosystem functions and is key to achieving the state’s coequal goals of “providing a more reliable water supply for California and protecting, restoring and enhancing the Delta ecosystem … in a manner that protects and enhances … the values of Delta as an evolving place”. The economic, ecological, and social costs of scientific uncertainty in water management controversies are significant - and to some degree unavoidable. Scientific findings that relate fishes and flows increasingly guide decisions on how to manage flows for the well-being of threatened or endangered species in the Delta. Many studies – and management decisions – rely on correlations between water flows and fish populations. But the decisions warrant fuller understanding of precisely how the flows affect the fishes. Knowledge of these underlying mechanisms is likely to facilitate adaptive management by clarifying uncertainty and risk, by creating specific expectations for outcomes and by strengthening testable hypotheses. This report therefore recommends, first and foremost (there are other recommendations as well), redoubling effects to identify causes and effects concerning fishes and flows in the Delta.

Focused groundwater recharge in the Amargosa Desert basin

U.S. Geological Survey (USGS) | July 1st, 2007

 The Amargosa River is an approximately 300-kilometer-long regional drainage connecting the northern highlands on the Nevada Test Site in Nye County, Nev., to the floor

 The Amargosa River is an approximately 300-kilometer-long regional drainage connecting the northern highlands on the Nevada Test Site in Nye County, Nev., to the floor of Death Valley in Inyo County, Calif. Streamflow analysis indicates that the Amargosa Desert portion of the river is dry more than 98 percent of the time. Infiltration losses during ephemeral flows of the Amargosa River and Fortymile Wash provide the main sources of ground-water recharge on the desert-basin floor. The primary use of ground water is for irrigated agriculture. The current study examined ground-water recharge from ephemeral flows in the Amargosa River by using streamflow data and environmental tracers. The USGS streamflow-gaging station at Beatty, Nev., provided high-frequency data on base flow and storm runoff entering the basin during water years 1998–2001. Discharge into the basin during the four-year period totaled 3.03 million cubic meters, three quarters of which was base flow. Streambed temperature anomalies indicated the distribution of ephemeral flows and infiltration losses within the basin. Major storms that produced regional flow during the four-year period occurred in February 1998, during a strong El Niño that more than doubled annual precipitation, and in July 1999. The study also quantified recharge beneath undisturbed native vegetation and irrigation return flow beneath irrigated fields. Vertical profiles of water potential and environmental tracers in the unsaturated zone provided estimates of recharge beneath the river channel (0.04–0.09 meter per year) and irrigated fields (0.1–0.5 meter per year). Chloride mass-balance estimates indicate that 12–15 percent of channel infiltration becomes ground-water recharge, together with 9–22 percent of infiltrated irrigation. Profiles of potential and chloride beneath the dominant desert-shrub vegetation suggest that ground-water recharge has been negligible throughout most of the basin since at least the early Holocene. Surface-based electrical-resistivity imaging provided areal extension of borehole information from sampled profiles. These images indicate narrowly focused recharge beneath the Amargosa River channel, flanked by large tracts of recharge-free basin floor.

Food Web Fuel Differs Across Habitats and Seasons of a Tidal Freshwater Estuary

Estuaries and Coasts (Springer) | July 11th, 2020

Estuarine food webs are fueled by multiple different primary producers. However, identifying the relative importance of each producer to consumers is difficult, particula

Estuarine food webs are fueled by multiple different primary producers. However, identifying the relative importance of each producer to consumers is difficult, particularly for fishes that utilize multiple food sources due to both their mobility and their generally high trophic levels. Previous studies have documented broad spatial differences in the importance of primary producers to fishes within the Upper San Francisco Estuary, California, including separation between pelagic and littoral food webs. In this study, we evaluated the importance of primary producers to adult fishes in three closely spaced subregions that represented disparate habitat types (a tidal wetland channel, a turbid backwater channel, and a deep open-water channel), each a potential outcome of local restoration projects. Using stable isotope analysis coupled with a Bayesian mixing model, we identified significant differences in primary-producer contribution to fishes and invertebrates across habitats and seasons, especially in the relative contribution of submersed aquatic vegetation and phytoplankton. Most fishes utilized multiple primary producers and showed little segregation between pelagic and littoral food webs among habitats. Availability of primary producers differs seasonally and across multiple spatial scales, helping to buffer environmental variability and thus enhancing food web resilience. Ecosystem restoration may improve with emphasis on restoring a wide variety of primary producers to support consumers.

Fracturing dams, fractured data: Empirical trends and characteristics of existing and removed dams in the United States

River Research and Applications (Wiley) | May 20th, 2018

Dam removals in the United States continue to accelerate in pace and scope, but no national analyses have examined how removed dams compare with existing dam stock. Here,

Dam removals in the United States continue to accelerate in pace and scope, but no national analyses have examined how removed dams compare with existing dam stock. Here, we review and analyse the best available national data on dams from the National Inventory of Dams (NID), dam removals from American Rivers, the U.S. Geological Survey, and the National River Restoration Science Synthesis databases to compare trends and characteristics of removed versus existing dams in the United States. If historical trends continue, by 2050 the United States can expect between 4,000 and 36,000 total removals, including 2,000–10,000 removals of NID dams. Best‐fit regression models estimate total costs between $50.5 million and $25.1 billion (mean $10.5 billion, median $416.5 million) for all removals and $29.6 million to $18.9 billion (mean $7.2 billion, median $285 million) for NID removals, a significant cost savings over present stated dam rehabilitation needs. Structural characteristics and ages of documented removals are not representative of existing dams, with privately owned hydroelectric dams subject to public oversight and water supply dams the most disproportionately removed. We conclude that dam removal science would benefit from the creation of an interdisciplinary framework for studying dams as environmental, social, and technological interventions, facilitated by transparent datasets around dams and removals and reflexive research approaches that combine statistical approaches with place‐based analyses.

Framework to Coordinate Water Quality Improvement and Wildlife Habitat Conservation to Protect California Streams, Wetlands and Riparian Areas

San Francisco Estuary Institute (SFEI) | February 1st, 2016

The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management pr

The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management programs provides an opportunity for their coordination to better protect California’s aquatic resources, especially streams, wetlands, and riparian areas. Such coordination is patently desirable. A framework has been developed to help coordinate restoration and compensatory mitigation across policies governing wildlife conservation and water quality in the landscape context. The framework is based on the Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW) of the Water Quality Monitoring Council. The framework presented here is a version of the standard WRAMP framework. It only differs from the standard framework to better accommodate wildlife conservation planning, assessment and reporting. To distinguish this version from the standard version, it is termed theWRAMP for wildlife (WRAMPw).

French Creek Flow Accounting Study

Scott River Water Trust | May 15th, 2020

The Scott River Water Trust (SRWT) has been working with adjudicated water-users in Scott Valley since 2007 to develop opportunities for stream flow enhancement through t

The Scott River Water Trust (SRWT) has been working with adjudicated water-users in Scott Valley since 2007 to develop opportunities for stream flow enhancement through temporary leases or long-term/permanent dedications of surface water rights. Under the seasonal Water Leasing Program, the SRWT contracts with voluntary agricultural producers to temporarily forbear all or part of their decreed water right(s) during the irrigation season in exchange for fair financial compensation. The purpose of the seasonal Water Leasing Program is to improve conditions for anadromous fish in priority stream reaches during critical life stages and time periods. The Siskiyou Resource Conservation District (SRCD) has been integrally involved with implementation of the seasonal Water Leasing Program since its inception and particularly with the monitoring component. Monitoring of seasonal transactions is generally limited to ensuring compliance with the lease terms and confirming stream response. However, in 2016 the SRWT proposed expanding the scope of effectiveness monitoring associated with the Water Leasing Program based on suggestions from Andrew Purkey and Rankin Holmes of the National Fish and Wildlife Foundation and their experience monitoring transactions in the Columbia River Basin (Holmes, et al., 2013). Under funding from the California Flow Restoration Accounting Fund managed by the National Fish and Wildlife Foundation, the SRWT contracted with the SRCD to explore several additional effectiveness monitoring techniques on French Creek including instream water level/discharge monitoring, wetted- perimeter analysis and alluvial connectivity surveillance. The purpose of this additional monitoring was to evaluate the applicability and effectiveness of these techniques to stream flow enhancement in Scott Valley and determine whether it would make sense for the SRWT adopt these practices into its programs. The specific components and objectives of the work completed on French Creek included: • Evaluate the instream effect of forbearance agreements performed by SRWT • Establish and maintain monitoring stations throughout French Creek to determine the downstream extent that returned water from various leases had on stream flow and temperature • Perform wetted perimeter analysis on French Creek to develop a relationship between instream flows and aquatic habitat conditions • Conduct periodic fisheries surveys through French Creek to evaluate the relative abundance of salmonids influenced by the transactions • Conduct periodic foot surveys through lower French Creek to establish the temporal and spatial connectivity to the Scott River This report summarizes the monitoring and analysis conducted by the SRCD during the 2018 and 2019 water leasing seasons under the French Creek Flow Accounting Study and provides conclusions related to the applicability of these methods to the SRWT.

Friant Water Supply Protection Association vs. Del Puerto Water District et al

Superior Court of California, County of Stanislaus | October 31st, 2022