Sacramento River

An Index of Biotic Integrity (IBI) for Perennial Streams in California’s Central Valley

California State Water Resources Control Board (SWRCB) | December 1st, 2008

Bioassessment is the science of using aquatic organisms as indicators of ecological condition in streams in rivers. Many types of organisms can be used as indicat

Bioassessment is the science of using aquatic organisms as indicators of ecological condition in streams in rivers. Many types of organisms can be used as indicators, for example fish or algae, but bioassessment is most frequently based on benthic macroinvertebrates (BMIs), which are small but visible bottom-dwelling organisms such as insects. BMI data sets typically consist of long lists of species (or taxa) found in a sample and their relative abundances. These data can be simplified into measures of biological condition such as indices of biotic integrity (IBIs) that are designed to be sensitive to human-caused alterations to the landscape, to stream channels and riparian zones, and to water chemistry. IBIs function much like economic indicators: high IBI scores reflect good ecological conditions while low IBI scores reflect poor ecological conditions. Bioassessment is increasingly used throughout California by water quality monitoring programs, but in the Central Valley bioassessment is more challenging than in other regions of the state because the entire landscape and most streams are highly altered by human activities such as urbanization, agriculture and water diversions. This makes it impossible to evaluate how BMIs respond across a complete gradient of human disturbance within the region, that is, from minimally disturbed reference sites where human activity is absent or minimal and which therefore set the benchmark for biological expectations, to the most altered sites with degraded biology. In the Central Valley, minimally disturbed reference sites are no longer available. Even the ‘least-disturbed’ sites, which represent the best-available chemical, physical and biological habitat conditions given the current state of the landscape, are markedly disturbed. Reference sites in other parts of California, such as the Sierra Nevada or the Sierra foothills, may be significantly less disturbed than Central Valley reference sites. In this study, BMI data sets from 11 studies conducted at various intervals over the last 14 years were compiled to build an IBI for Central Valley streams. Data were not collected consistently by the different studies, and many gaps were present in associated physical habitat and water chemistry data sets. This could be corrected for BMI samples by standardizing to a consistent level of taxonomic effort. Gaps in other data could not be addressed. Criteria for defining ‘best-available’ reference sites were established as data allowed and were based on local urban and agricultural intensity, stream channel and riparian condition, and stream substrate composition. Eighty BMI metrics were evaluated for inclusion in the IBI based on 4 criteria: 1) sufficient range for scoring; 2) responsiveness to land use and/or local disturbance variables measured at the 150-meter sampling reach (as data allowed); 3) good discrimination between reference and test sites; 4) lack of correlation with other responsive metrics. Five final metrics were selected and scored for inclusion in the IBI: collector richness (number of taxa that are collector- feeders), predator richness (number of taxa that are predators), percent EPT taxa (percent of taxa that are mayflies, stoneflies, or caddisflies), percent clinger taxa (percent of taxa that cling to vegetation) and Shannon diversity (a composite measure of taxonomic richness and evenness of abundance). The final IBI showed good discrimination between reference and test sites, and was validated with an independent data set. BMI metrics and the final IBI were more strongly related to reach-scale physical habitat variables than to water chemistry or land use variables, but detailed water chemistry was lacking for many sites, and some studies have shown that response to land use diminishes when more than 10% of a watershed is degraded by human activities. Despite data gaps that were less than ideal for indicator development, this study is the first to set expectations for Central Valley BMI assemblages based on best-available reference sites. The Central Valley IBI can be used as a general interpretive framework for benthic samples collected from perennial streams on the valley floor and provides an objective means for rating biological condition in a region with high urban and agricultural intensity. The ability to rank sampling sites relative to explicitly defined biological expectations is essential to any biological monitoring program. Therefore, this index may prove useful in several monitoring applications, including California’s non- point source CMAP program where sampling was stratified to assess and compare stream condition in urban, agricultural and forested watersheds, in stormwater monitoring programs, in point-source pollution investigations, and in stream restoration monitoring. Key recommendations include: 1) that all future bioassessment projects in the Central Valley should collect quantitative physical habitat and water chemistry with consistent protocols at all sites; in situ chemistry and rapid (qualitative) physical habitat are not sufficient for screening reference sites or evaluating BMI responses to stressor gradients; 2) that bioassessment should be added to NPS monitoring where programs are already collecting more intensive stressor data such as pesticides, nutrients and metals. This will provide California’s monitoring programs with better datasets to support future analyses.

An Introduction to High-Frequency Nutrient and Biogeochemical Monitoring for the Sacramento– San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Jo

This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). This first report provides an introduction to the reasons for and fundamental concepts behind collecting HF measurements, and describes the benefits associated with a real-time, continuous, HF, multi-parameter water quality monitoring station network that is co-located with flow stations. It then provides examples of how HF nutrient measurements have improved our understating of nutrient sources and cycling in aquatic systems worldwide, followed by specific examples from the Delta. These examples describe the ways in which HF instrumentation may be used for both fixed-station and spatial assessments. The overall intent of this document is to describe how HF measurements currently (2017) are being used in the Delta to examine the relationship between nutrient concentrations, nutrient cycling, and aquatic habitat conditions.

An overview of multi-dimensional models of the Sacramento-San Joaquin Delta

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

Over the past fifteen years, the development and application of models in San Francisco Bay and the Sacramento-San Joaquin Delta has transformed our ability to analyze an

Over the past fifteen years, the development and application of models in San Francisco Bay and the Sacramento-San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta in the future. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship between X2, flow, fish abundance, and the low salinity zone. Through modeling, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This chapter provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multidimensional models to predict how future Delta conditions will affect both fish and water supply.  

Anadromous Salmonids in the Delta: New Science 2006-2016

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

As juvenile salmon enter the Delta, they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migrati

As juvenile salmon enter the Delta, they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this channel network were limited. Fortunately, thanks to technological advances, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis have provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use the Delta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

Anderson Subbasin Groundwater Sustainability Plan

Enterprise Anderson Groundwater Sustainability Agency | January 20th, 2022

This GSP covers all of the 98,700 acres of the Anderson Subbasin. The GSP describes the current groundwater conditions and hydrogeologic conceptual model, establishes a

This GSP covers all of the 98,700 acres of the Anderson Subbasin. The GSP describes the current groundwater conditions and hydrogeologic conceptual model, establishes a water budget, outlines local sustainable management criteria (SMC or SMCs), and describes projects and management actions for maintaining sustainability through the GSP planning and implementation period. Due to size, this file has been divided into 9 parts. Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9

Anderson-Cottonwood Irrigation District Integrated Regional Water Management Program – Groundwater Production Element Project

U.S. Bureau of Reclamation (USBR) | August 15th, 2011

This project would improve the flexibility and reliability of the District’s water supply, particularly during dry and critically dry water years. In 2004, ACID’s sur

This project would improve the flexibility and reliability of the District’s water supply, particularly during dry and critically dry water years. In 2004, ACID’s surface water rights were reduced from 165,000 to 121,000 ac-ft per year as part of the renegotiation of the 40-year Settlement Contract. Furthermore, the west side of the District’s system has little to no downstream control. Control of the system is achieved at the head of the 35-mile main canal, causing some delivery difficulties at the downstream end of the service area. By pushing water from upstream to downstream without an ability to manage intermediate water surface elevations, downstream response time to water delivery needs can be greatly hindered. This project would help with the flexibility and reliability required to meet agricultural water needs.

Annual Report of Activities October 1, 2013 to September 30, 2014, American River Group (ARG)

Delta Stewardship Council (Delta Council) | September 30th, 2014

Annual Report of Activities October 1, 2013, to September 30, 2014, Delta Operations for Salmonids and Sturgeon (DOSS) Technical Working Group

Delta Stewardship Council (Delta Council) | October 31st, 2014

Annual Report of Activities Water Year 2018 Stanislaus Operations Group (SOG)

Delta Stewardship Council (Delta Council) | November 1st, 2018

Anthropogenic warming drives earlier wildfire season onset in California

American Association for the Advancement of Science (AAAS) | August 8th, 2025

Annual wildfire area in California has rapidly grown in recent decades, with increasingly negative impacts on people. The fire season is also lengthening, with an earlier

Annual wildfire area in California has rapidly grown in recent decades, with increasingly negative impacts on people. The fire season is also lengthening, with an earlier onset. This trend has been hypothesized to be driven by anthropogenic warming, but it has yet to be quantitatively attributed to climate drivers. Using a comprehensive fire occurrencedataset, we analyze fire season onset and climate controls on its variability and change during 1992–2020 in 13 California ecoregions. Northern California ecoregions show stronger trends toward earlier onset compared to more arid southern California ecoregions. Onset has trended earlier for all but one ecoregion. Interannual variability of onset is dominated by climate variability and its influence on fuel moisture. Trend attribution inferred from onset-climate relationships suggests that anthropogenic warming advanced fire season onset by 6 to 46 days during 1992–2020 in 11of 13 ecoregions. Continued warming is expected to further promote earlier fire season onsets.