Adaptation of a reference site selection methodology to creeks and sloughs of California’s Sacramento Valley and alternative strategies for developing a regional bioassessment framework

Central Valley Regional Water Quality Control Board (CVRWQCB) | November 14th, 2005

Bioassessment has shown significant promise as an effective tool for ambient water quality management in many regions of California. However, the scale and intensity of l

Bioassessment has shown significant promise as an effective tool for ambient water quality management in many regions of California. However, the scale and intensity of landscape and water transport alteration in the Central Valley pose substantial challenges to implementing bioassessment to its full potential in the region. Bioassessment programs usually are established around a careful characterization of regional reference conditions, which can be defined as the condition of waterbodies that are least impaired by human activities. The reference condition defines a benchmark against which to infer biological impairment and to set expectations for biotic condition. Although there are several techniques available for determining reference condition, by far the most commonly applied is the use of reference sites, which are used to establish the range of natural variability in biotic condition. We investigated the potential for identifying reference sites for segments of sloughs and creeks of the Sacramento Valley at elevations less than 85 meters. We describe here the results of a pilot study designed to adapt an existing reference site selection methodology for use in the Central Valley. Potential reference sloughs and creeks were selected on the basis of a suite of visual assessments of riparian and instream condition and qualitative GIS-based land use data. Analysis of the benthic macroinvertebrate (BMI) assemblages collected from 30 targeted reference sites (23 creeks and 7 sloughs) was focused on addressing two main questions: 1) should creeks and sloughs be considered unique waterbody classes for the purposes of bioassessment?, 2) what is the potential for reference site based bioassessment in valley waterbodies? We addressed these questions with the BMI data using a combination of direct metric comparisons and NMS ordination. To improve our ability to interpret patterns at our 30 sites, we included two additional datasets of BMI data recently collected from nearby waterbodies. We drew three general conclusions from this study: 1) the adaptation of reference site selection to Central Valley streams was effective; we were able to find sites in the valley to use as reference and there is enough diversity in the BMI assemblages at these reference sites to use them to detect impairment, 2) although creeks and sloughs may need to be treated as separate classes of waterbodies for bioassessment-based regulation, there is evidence to suggest that the differences are not clear-cut and the question needs further investigation, 3) BMI assemblages in valley floor reference sites are clearly different from those in foothill reference sites. We discuss the potential for reference site based determination of reference conditions and summarize the current state of the science for defining reference condition in regions without adequate reference sites. We also list a set of recommendations that the Central Valley Regional Water Quality Control Board should consider while constructing a defensible framework for bioassessment in the Central Valley.

Advancement of Salinity and Flow Monitoring in the San Francisco Bay Delta, San Francisco Bay Delta Action Plan Implementation Support, FINAL REPORT

U.S. Geological Survey (USGS) | February 1st, 2017

This report evaluates the cost and utility of adding coupled surface and near-bottom salinity monitors along the axis of the San Francisco Estuary, and the types

This report evaluates the cost and utility of adding coupled surface and near-bottom salinity monitors along the axis of the San Francisco Estuary, and the types of equipment and approximate costs of this additional monitoring effort. Expanding the monitoring network by adding downstream monitoring stations, adding stations at depth, and increasing the resolution of monitoring stations along the axis of the estuary will generate data that capture tidal dynamics and may be used to derive equations that predict salinity and other hydrodynamic endpoints with greater precision than currently possible. The proposed monitoring is expected to enhance the hydrodynamic modeling of the salt field and the accuracy of compliance and prediction methods in the estuary. Springtime outflows through the San Francisco Estuary are managed through the position of the 2 parts per thousand bottom salinity isohaline (X2) along the center-line of the estuary, measured in kilometers relative to the Golden Gate Bridge. X2 is calculated from surface salinity measurements with a constant vertical conversion factor. The current framework of sampling stations does not collect near-bottom salinity along the estuary center-line, does not extend far enough down-estuary to adequately characterize X2 during high flows, and the separation of monitoring locations limits the precision with which the position of X2 can be calculated. Near-surface and near-bed salinity and turbidity sensors and ancillary hardware could be added to the estuary for an estimated cost of ~ $780K in capital costs and $500K/yr in operation, maintenance, and data processing costs based on a proposed addition to an existing surface salinity network in San Francisco Estuary operated by the US Geological Survey. While this document does not recommend a particular plan for implementation, the compiled information provides rough costs for planning considerations. Data collected through a network of this kind could improve precision of compliance methods with the existing Delta outflow standard. With data collected over time, it would support modifications to a new/modified Delta outflow standard, improve our ability to assess the effectiveness of water quality standards, and improve protection of water supply and aquatic life habitat. These data would also improve the salinity modeling capability and accuracy for future predictions and past evaluations. Expanding the monitoring network also provides a platform to connect hydrodynamic and biological measurements which is necessary for integrating biological and hydrodynamic modeling and advancing knowledge of estuarine mechanisms that influence fish population trends. The specific design of a monitoring network and whether or not the improvements can be optimized for their potential outputs was beyond the scope of the present document and needs to be based on a broader discussion among science experts, regulators, and the regulated community.

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.

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

Annual Owens Valley Operations Plan for the 2024-25 Runoff Year

Los Angeles Department of Water & Power (LADWP) | June 20th, 2024

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, October 1, 2013 to September 30, 2014, Stanislaus Operations Group (SOG)

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

Applied Aquatic Science: A Business Plan for EcoAtlas

San Francisco Estuary Institute (SFEI) | March 7th, 2017

The EcoAtlas suite of tools represents a significant investment of time, energy, thought, scientific testing, technical innovation, and capital from a number of state and

The EcoAtlas suite of tools represents a significant investment of time, energy, thought, scientific testing, technical innovation, and capital from a number of state and federal public agencies, grant programs, and NGOs over the course of its 17-year existence. The toolset embodies the scientific and programmatic investments of the California Wetland Monitoring Workgroup (CWMW), its many related state and federal agencies, non-governmental organizations (NGOs), and private consultants, as well as the goals of the growing set of stakeholders who have expanded the circle of interested parties over the years. It is known by many names -- “WRAMP” being most common -- but in its essence it comprises the following tools:  ● EcoAtlas map viewer ● Project Tracker ● The California Aquatic Resources Inventory (CARI) map and editor tool ● The California Rapid Assessment Method (CRAM) ● The Riparian Zone Estimator Tool (RipZET) Now highly capable, the toolset represents more than science and technology alone, but a distillation of both, customized to meet specific goals associated with the landscape-scale tracking and characterization of California’s aquatic resources. The US Environmental Protection Agency (US EPA), for instance, has supported the toolset through multiple development grants so that the collected tools might be complementary to a still-nascent, statewide wetland protection program. Meanwhile, the state’s Coastal and Delta Conservancies require the use of the tool, and regional water boards -- including SF Bay, Lahontan, and North Coast -- regularly employ the tool for mitigation and restoration project tracking. Essentially, EcoAtlas has proven critical to a variety of programs and represents a successful product of broad-based collaboration. However, it currently stands at a crossroads, and its stakeholders must direct the toolset’s future. The following plan is intended to ensure the continued vitality of the toolset. The plan’s success will depend upon the continued collaboration of the public agencies that have supported the toolset thus far, but it must also integrate principles of resilience as it accounts for the tensions that arise as organizations move in different strategic directions. 

Aquifer-system compaction and land subsidence: Measurements, analyses, and simulations-the Holly Site, Edwards Air Force Base, Antelope Valley, California

U.S. Geological Survey (USGS) | July 1st, 2000

Arsenic, chromium, uranium, and vanadium in rock, alluvium, and groundwater, Mojave River and Morongo Areas, western Mojave Desert, southern California

U.S. Geological Survey (USGS) | October 16th, 2023

Trace elements within groundwater that originate from aquifer materials and pose potential public-health hazards if consumed are known as geogenic contaminants. The geoge

Trace elements within groundwater that originate from aquifer materials and pose potential public-health hazards if consumed are known as geogenic contaminants. The geogenic contaminants arsenic, chromium, and vanadium can form negatively charged ions with oxygen known as oxyanions. Uranium complexes with bicarbonate and carbonate to form negatively charged ions having aqueous chemistry similar to oxyanions. The concentrations of arsenic, chromium, uranium, and vanadium in groundwater result from the combined effects of (1) geologic abundance within aquifer materials; (2) the fraction of these elements that have weathered from and sorbed to the surfaces of mineral grains and are potentially available to groundwater; and (3) the aqueous chemistry of dissolved oxyanions in groundwater during different redox conditions and pH, both of which are affected by hydrogeology, including the length of time groundwater has been in contact with aquifer materials. Concentrations of arsenic, chromium, uranium, and vanadium were measured in samples of (1) rock, surficial alluvium, and drill cuttings using portable (handheld) X-ray fluorescence (pXRF); (2) operationally defined fractions extractable from these materials; and (3) water from wells sampled between 2000 and 2018 within the 3,500 square mile Mojave River area and Morongo area of the western Mojave Desert, southern California.