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 Innovative Scheme to Confront the Trade-Off Between Water Conservation and Heat Alleviation With Environmental Justice for Urban Sustainability: The Case of Phoenix, Arizona

American Geophysical Union (AGU) | February 17th, 2023

An integrated framework for stormwater management and life cycle assessment of rainwater harvesting: A comparative study of two underserved communities

Science of the Total Environment (Elsevier) | November 4th, 2024

An Integrated Surface Water-Groundwater Interaction Model for the Carmel River

California State University, Monterey Bay | April 30th, 2010

The Carmel River supplies fresh water to the residents of the Monterey Peninsula within the water district served by the California American Water company (Cal-Am). The S

The Carmel River supplies fresh water to the residents of the Monterey Peninsula within the water district served by the California American Water company (Cal-Am). The State Water Resources Control Board, in 1995, ordered that Cal-Am reduce their annual diversions from the Carmel River Watershed to within legal right (3,376 acre-feet per year). An alternative water source to the Carmel River has yet to be determined, and as a result, Cal-Am must continue to divert more water than their legal entitlement. The current magnitude of diversions has a negative impact on the spawning and migrating habitat of Steelhead (Oncorhynchus mykiss). Existing software in the Tarsier Environmental Modeling Framework was used to model the spatial distribution of surface water along the Carmel River. The model simulated the flow of water downstream from catchment area to the Pacific Ocean. The river channel was represented by a network data set comprised of links, representing individual reaches of the river, connected by nodes. Prior to my work, systematic error in the model was thought to be partially the result of the model lacking a simulation of the interactions between the surface water and the underlying aquifer. A groundwater sub-model was developed to correct for the systematic error. The groundwater sub-model simulated the movement of water between the river channel and the aquifer. Stock variables representing a shallow and deep aquifer were added to each link of the network data set. Simulated water in the surface water stock of each link percolates to these aquifer stocks until the groundwater reaches aquifer capacity, allowing surface water to continue flowing downstream. The model also allows the lateral flow of groundwater according to Darcy’s Law. Quantitative and qualitative analysis of model output compared to observed data showed an increase in model accuracy. Quantitatively, a Nash- Sutcliff Coefficient was improved from 0.88 to 0.97 with the addition of the groundwater model. Qualitatively, a visualization of the longitudinal profile of the river system showed the simulated aquifer controlling the surface flow. A hypothetical application of this model is presented where reducing the pumping rate from the aquifer allowed the wetted river channel to increase by 2.5 km. Future work on the model should include a reservoir sub-model and accounting for spatial variability in the precipitation throughout the catchment area. With these improvements it will be possible to improve predictions of the spatial distribution of surface water along the Carmel River given hypothetical scenarios such as the rate and spatial distribution of pumping from the Carmel Aquifer. Using these simulations to inform decisions of river management could benefit all stakeholders of the river.

An Introduction to EcoAtlas: Applied Aquatic Science

San Francisco Estuary Institute (SFEI) | September 14th, 2016

The term “EcoAtlas” has been in use for over 20 years in association with the study, assessment, and reporting of aquatic resources in California. What began as “W

The term “EcoAtlas” has been in use for over 20 years in association with the study, assessment, and reporting of aquatic resources in California. What began as “Wetland Tracker” in 2000, with its goal of recording essential information about wetland restoration projects in the greater Bay Area, later blossomed into a broad technological ecosystem of interrelated tools, each focused on delivering specialized, program-focused features, as defined by key stakeholder groups. Having evolved over time, EcoAtlas comprises a diverse toolset, but the collection shares common libraries, common approaches, and common development methodologies. Though each emerged from different funding opportunities and requirement drivers, the toolset collectively addresses a synthesized “whole watershed approach.” Whether estimating the ideal riparian buffer width for a given stream or assessing the health of a wetland at the edge of the estuary, the EcoAtlas tools allow practitioners to deploy the right tool for the job across the entire watershed, thereby producing a complete picture through composite outputs.

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 Introduction to the San Francisco Estuary

Bay Institute | April 8th, 2012

San Francisco Bay enters most of our lives as an obstacle to pass over as quickly as traffic-choked bridges allow. Although this beats earlier attitudes—when we saw the

San Francisco Bay enters most of our lives as an obstacle to pass over as quickly as traffic-choked bridges allow. Although this beats earlier attitudes—when we saw the Bay mainly as a dumping ground, a dam site, or a pit to fill in and pave over—we remain largely oblivious to one of the most remarkable wild resources in urban North America. Beneath our wheels lies a world of interesting and outlandish life, with much that puzzles even the scientists who regularly plumb its depths.

An ongoing shift in Pacific Ocean sea level

American Geophysical Union (AGU) | July 30th, 2016

Based on the satellite altimeter data, sea level off the west coast of the United States has increased over the past 5 years, while sea level in the western tropical Pac

Based on the satellite altimeter data, sea level off the west coast of the United States has increased over the past 5 years, while sea level in the western tropical Pacific has declined. Understanding whether this is a short-term shift or the beginning of a longer-term change in sea level has important implications for coastal planning efforts in the coming decades. Here, we identify and quantify the recent shift in Pacific Ocean sea level, and also seek to describe the variability in a manner consistent with recent descriptions of El Nino-Southern Oscillation (ENSO) and particularly the Pacific Decadal Oscillation (PDO). More specifically, we extract two dominant modes of sea level variability, one related to the biennial oscillation associated with ENSO and the other representative of lower-frequency variability with a strong signal in the northern Pacific. We rely on cyclostationary empirical orthogonal function (CSEOF) analysis along with sea level reconstructions to describe these modes and provide historical context for the recent sea level changes observed in the Pacific. As a result, we find that a shift in sea level has occurred in the Pacific Ocean over the past few years that will likely persist in the coming years, leading to substantially higher sea level off the west coast of the United States and lower sea level in the western tropical Pacific.

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.  

An unprecedented coastwide toxic algal bloom linked to anomalous ocean conditions

American Geophysical Union (AGU) | October 9th, 2016

A coastwide bloom of the toxigenic diatom Pseudo-nitzschiain spring 2015 resulted in the largest recorded outbreak of the neurotoxin, domoic acid, along the North Ameri

A coastwide bloom of the toxigenic diatom Pseudo-nitzschiain spring 2015 resulted in the largest recorded outbreak of the neurotoxin, domoic acid, along the North American west coast. Elevated toxins were measured in numerous stranded marine mammals and resulted in geographically extensive and prolonged closures of razor clam, rock crab, and Dungeness crab fisheries. We demonstrate that this outbreak was initiated by anomalously warm ocean conditions. Pseudo-nitzschia australis thrived north of its typical range in the warm, nutrient-poor water that spanned the northeast Pacific in early 2015. The seasonal transition to upwelling provided the nutrients necessary for a large-scale bloom; a series of spring storms delivered the bloom to the coast. Laboratory and field experiments confirming maximum growth rates with elevated temperatures and enhanced toxin production with nutrient enrichment, together with a retrospective analysis of toxic events, demonstrate the potential for similarly devastating ecological and economic disruptions in the future.