San Joaquin 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.

Analyses of Rotary Screw Trap Sampling of Migrating Juvenile Chinook Salmon in the Stanislaus River, 1996-2005

Delta Stewardship Council (Delta Council) | August 1st, 2006

Analysis and simulation of regional subsidence accompanying groundwater abstraction and compaction of susceptible aquifer systems in the USA

Mexican Geological Society (Sociedad Geológica Mexicana) | January 17th, 2013

Regional aquifer-system compaction and land subsidence accompanying groundwater abstraction in susceptible aquifer systems in the USA is a challenge for managing groundwa

Regional aquifer-system compaction and land subsidence accompanying groundwater abstraction in susceptible aquifer systems in the USA is a challenge for managing groundwater resources and mitigating associated hazards. Developments in the assessment of regional subsidence provide more information to constrain analyses and simulation of aquifer-system compaction. Current popular approaches to simulating vertical aquifer-system deformation (compaction), such as those embodied in the aquitard drainage model and the MODFLOW subsidence packages, have proven useful from the perspective of regional groundwater resources assessment. However, these approaches inadequately address related local-scale hazards—ground ruptures and damages to engineered structures on the land surface arising from tensional stresses and strains accompanying groundwater abstraction. This paper presents a brief overview of the general approaches taken by the U.S. Geological Survey toward understanding aquifer-system compaction and subsidence with regard to a) identifying the affected aquifer systems; b) making regional assessments; c) analyzing the governing processes; and d) simulating historical and future groundwater flow and subsidence conditions. Limitations and shortcomings of these approaches, as well as future challenges also are discussed 

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

Annual Report of Activities, October 1, 2013 to September 30, 2014, Stanislaus Operations Group (SOG)

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

Anthropogenic warming impacts on California snowpack during drought

American Geophysical Union (AGU) | March 15th, 2017

Sierra Nevada climate and snowpack is simulated during the period of extreme drought from 2011 to 2015 and compared to an identical simulation except for the removal of t

Sierra Nevada climate and snowpack is simulated during the period of extreme drought from 2011 to 2015 and compared to an identical simulation except for the removal of the twentieth century anthropogenic warming. Anthropogenic warming reduced average snowpack levels by 25%, with middle‐to‐low elevations experiencing reductions between 26 and 43%. In terms of event frequency, return periods associated with anomalies in 4 year 1 April snow water equivalent are estimated to have doubled, and possibly quadrupled, due to past warming. We also estimate effects of future anthropogenic warmth on snowpack during a drought similar to that of 2011–2015. Further snowpack declines of 60–85% are expected, depending on emissions scenario. The return periods associated with future snowpack levels are estimated to range from millennia to much longer. Therefore, past human emissions of greenhouse gases are already negatively impacting statewide water resources during drought, and much more severe impacts are likely to be inevitable.