View SCCWRP’s full thematic Research Plan for Bioassessment (PDF)
2026-2027 Executive Summary
Biological assessment, or bioassessment, is the science of evaluating the health of an ecosystem by assessing the organisms that live within it. In aquatic ecosystems, algae and invertebrates serve as particularly useful indicators of ecosystem health because they are relatively sessile and live along bottom habitats where chemical and other stressors often concentrate. Unlike traditional physical or chemistry-based monitoring, which provides only limited information about a relatively narrow set of pollutants in the environment at a discrete point in time, living organisms reflect the combined impact of multiple stressors over time. Consequently, bioassessment has the potential to provide a more integrated reflection of the condition of an aquatic ecosystem. Bioassessment also is a direct measure of aquatic life, and thus more closely tied to environmental managers’ end-goal focus on ecosystem protection. SCCWRP is focused on developing an overall bioassessment framework (e.g., survey design, interpretation methods) and associated tools that environmental managers can use to assess the health of aquatic ecosystems and inform regulatory and management decisions. SCCWRP has made considerable progress on developing bioassessment tools for streams, wetlands, and marine environments for a range of organisms, including benthic invertebrates, fish and algae. In addition to developing traditional morphologic methods for identifying organisms, SCCWRP also is developing complementary molecular methods – including environmental DNA (eDNA) – that have the potential to generate additional insights faster and more cost-effectively than traditional bioassessment methods, including improving understanding of interactions between communities. SCCWRP’s long-term goal is to develop bioassessment tools for all priority aquatic habitats using a wide range of indicators.
SCCWRP’s bioassessment work revolves around three main research areas: (1) condition assessments, which encompasses developing multiple bioassessment tools and methods to evaluate and quantify the condition of multiple water body types with both traditional and next-generation molecular methods; (2) causal and protective assessments, which encompasses applying bioassessment data and analyses to diagnose potential causes of water body impairment and vulnerabilities of healthy water bodies to future impairment, respectively, and (3) supporting the incorporation of bioassessment tools into management applications through facilitating data production, interpretation, and communication. To ensure condition and causal assessments are used to guide management decision aimed at improving overall condition, SCCWRP develops synthesis and integration tools that can translate and interpret bioassessment data and findings to actionable information. In particular, SCCWRP focuses on developing bioassessment interpretation frameworks to help managers understand how to use bioassessment results to inform decision-making, and how to connect bioassessment results to designated beneficial uses for water bodies.
This year, SCCWRP will continue to develop, refine, and expand its capacity to conduct both condition assessments and causal/protective assessments, as well as pursue development of guidance and decision support tools to inform management actions. SCCWRP’s focus for 2026-2027 will be on:
- Expanding capacity to assess water bodies: Building on past successes developing bioassessment indices for freshwater and marine ecosystems, SCCWRP is developing capacity to expand bioassessment tools to assess other water body types. SCCWRP’s priorities include the development of indices for estuarine habitats and for seagrass meadows, as well as the validation of tools in intermittent and ephemeral streams. . This research involves the development of sampling methods, taxonomic standardization protocols, creation of indices or other interpretive tools, and statistical analysis of the natural factors that affect the composition of biological communities.
- Understanding factors that affect biological conditions in constrained systems: Through regional monitoring and SCCWRP research, SCCWRP has extensively documented the poor biological conditions typically found in streams that flow through channels that have been modified for flood protection, water conveyance, and other uses. SCCWRP is building on this scientific foundation by examining the factors that affect conditions in these channels, so that strategies to improve conditions can be identified. This work will shed light on whether water quality improvements and/or flow management can benefit streams where modifications remain in place, as well as the potential impact of channel restoration. In parallel, SCCWRP is investigating whether modifications to estuaries – which, like streams, have been extensively modified in Southern California – can have an effect on ecological health.
- Integrating molecular methods: SCCWRP will continue to develop and integrate molecular methods into monitoring and assessment programs, with a focus on eDNA, which enables managers to detect and track organisms using the DNA that they shed into their environment. To support the integration of eDNA into routine monitoring and assessment activities, SCCWRP is studying how eDNA moves through and ultimately degrades in the environment, and supporting expansion of DNA reference libraries to encompass more types of organisms and habitats. SCCWRP also is working to develop novel molecular indices for streams and continue to standardize methods for invasive and endangered species monitoring, as these organisms can be difficult or infeasible to monitor via traditional observation and sampling.
- Enabling causal and protective assessment: SCCWRP’s bioassessment research not only facilitates the detection of water bodies in poor biological condition, but it also works to identify the stressors causing the impacts (causal assessment) and the water bodies that are in good biological health but are vulnerable to degradation (protective assessment). SCCWRP is expanding Rapid Screening Causal Assessment (RSCA) tools that facilitate automated analysis from the watershed scale to regional and statewide applications. In addition, SCCWRP is expanding RSCA to incorporate a wider range of stressors, such as flow alteration and toxic contamination, to support the broader integration of causal assessment into management programs. SCCWRP is also working toward developing a framework for supporting protective management actions, including identifying water bodies that have high conservation value and water bodies that are healthy but vulnerable to future stressor exposure. SCCWRP is focused on integrating a wide array of existing tools and data sources to provide a comprehensive assessment of present-day and future stresses on streams.
