Fishes, Hydrology, and Ecology of the Klamath River Basin

National Academy of Sciences (NAS) | February 11th, 2008

The Klamath River basin in southern Oregon and northern California is the focus of a prominent conflict over competing uses for water in the American West. Management mea

The Klamath River basin in southern Oregon and northern California is the focus of a prominent conflict over competing uses for water in the American West. Management measures for the protection of threatened and endangered fish species in the basin that have left less water available for irrigation have increased tensions among farmers and other stakeholders and brought into question the scientific justification of these measures. Two National Research Council studies evaluate a series of federal scientific assessments and recommend scientifically justified approaches to the problem.

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 Augmentations Modify an Estuarine Prey Field

University of California, Davis (UC Davis) | June 15th, 2023

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.

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.

Food Webs of the Delta, Suisun Bay, and Suisun Marsh: An Update on Current Understanding and Possibilities for Management

University of California, Davis (UC Davis) | October 1st, 2016

This paper reviews recent research findings on food web processes since 2008. It also highlights the idea of a changing baseline with respect to food web function. New re

This paper reviews recent research findings on food web processes since 2008. It also highlights the idea of a changing baseline with respect to food web function. New research indicates that interactions between habitat-specific food webs vary across the current landscape. For example, based on early work in the south Delta, the food web associated with underwater vegetation was thought to provide little support to species of concern; however, data from other regions of the estuary suggest that this conceptual model may not apply across the entire region. Habitat restoration has been proposed as a method of re-establishing historic food web processes to support species of concern. Benefits are likely for species that directly access such restored habitats, but are less clear for pelagic species. Several issues require attention to further improve the knowledge of food webs needed to support effective management, including: (1) synthesis of factors responsible for low pelagic biomass; (2) monitoring and research on effects of harmful algal blooms; (3) broadening the scope of long-term monitoring; (4) determining benefits of tidal wetland restoration to species of concern, including evaluations of interactions of habitat-specific food webs; and (5) interdisciplinary analysis and synthesis. The only certainty is that food webs will continue to change in response to the changes in the physical environment and new species invasions.

Fragmented kelp forest canopies retain their ability to alter local seawater chemistry

Nature Portfolio (Springer Nature) | July 20th, 2020

Kelp forests support some of the most productive and diverse ecosystems on Earth, and their ability to uptake dissolved inorganic carbon (DIC) allows them to modify loca

Kelp forests support some of the most productive and diverse ecosystems on Earth, and their ability to uptake dissolved inorganic carbon (DIC) allows them to modify local seawater chemistry, creating gradients in carbon, pH, and oxygen in their vicinity. By taking up both bicarbonate and CO2 as a carbon source for photosynthesis, kelp forests can act as carbon sinks, reducing nearby acidity and increasing dissolved oxygen; creating conditions conducive to calcification. Recent stressors, however, have reduced kelp forest canopies globally; converting once large and persistent forests to fragmented landscapes of small kelp patches. In a two-year study, we determined whether fragmented kelp patches retained the ability to alter local seawater chemistry. We found that diel fluctuations of multiple parameters of carbonate chemistry were greater in the kelp canopy than in the kelp benthos and in adjacent urchin barrens, consistent with metabolic activity by the kelp. Further, kelp fragments increased pH and aragonite saturation and decreased pCO 2 during the day to a similar degree as large, intact kelp forests. We conclude that small kelp patches could mitigate OA stress and serve as spatial and temporal refugia for canopy-dwelling organisms, though this effect is temporary and confined to daylight hours during the growing season.

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.