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Projects Worked On

Project Name Description
PISCES - Fish Distribution Tracking, Modelling, and Analysis

PISCES is software and data describing the best-known ranges for California's native fish. The data is compiled from multiple sources and experts and is stored and exported as rangemaps and summary maps. As of December 2013, it includes data on all of the state's 131 native fish taxa as well as 48 non-native species. You may obtain exported data for those taxa and compiled maps at If you are looking for the software itself, you can download the full software package (advanced computer abilities required) at

Management of the Spring Snowmelt Recession

In managed river systems in the Sierra Nevada, increased understanding of the fundamental relationships between the spring snowmelt flow regime and abiotic and biotic stream conditions is needed to aid water resource managers in making the complex decisions required to balance multiple water resource needs.

In this project, we seek to improve our understanding of the impacts of varying spring flow regimes on stream ecology, through empirical field studies, and water management, through hydropower optimization modeling.

Specifically, we are:

  1. assessing the effects of the spring flow regime on abiotic and biotic stream conditions through analyses of empirical field data at six river study sites with varying degrees of regulation, and
  2. applying and enhancing existing systems analysis techniques for multi-reservoir hydropower operations with ecologically meaningful instream flow constraints.

We expect the results from these tasks to be directly applicable in future relicensing projects where recent ecological knowledge and various modeling applications will be utilized to guide instream flow determinations.

We aim to provide resource managers not only with increased knowledge regarding the ecology of the spring recession, but with a series of methods that help predict the impacts of various spring flow regimes on the diversity of aquatic and riparian species and the economics of hydropower production.

Habitat Models for the Foothill Yellow-legged Frog

Resource managers use a variety of tools in hydropower relicensing to determine impacts from flow prescriptions on sensitive aquatic species. For the Foothill yellow-legged frog (Rana boylii), instream flow modeling is one tool that can be used to assess habitat suitability for egg mass and tadpole life stages. Several instream flow modeling methods are commonly used (e.g., one-dimensional habitat modeling, two-dimensional hydrodynamic models, and expert habitat mapping) and all modeling techniques require that habitat suitability be defined for each target species and lifestage. The models and criteria typically focus on three key characteristics of instream aquatic habitats – water depth, water velocity, and substrate – but may include habitat conditions.

This study compares commonly used methods of  defining habitat suitability criteria and applying those to instream flow models for R. boylii in the Sierra Nevada of California.  First, regional habitat suitability criteria (HSC) are developed using standard univariate and multivariate techniques, and the predictive performance and transferability of different HSC methods are evaluated. Second, three of the most commonly used instream flow assessment techniques are evaluated:  (1) one-dimensional habitat modeling, (2) two-dimensional hydrodynamic modeling, and (3) expert habitat mapping (judgement-based mapping by species experts).  A comparison table is provided to aid resource managers in selecting the most appropriate habitat assessment method for R. boylii given the specific conditions of a hydropower relicensing project.

Lastly, this project provides a compilation of recent literature and reports on basic ecology of R. boylii and effects of river regulation. This compilation is presented on a new website, hosted by the USDA Forest, Pacific Southwest Research Station and includes maps, a bibliography with abstracts, and tabular and narrative summaries: (

Code Library and Tools

As part of numerous other projects, Center for Watershed Sciences staff and researchers have developed code to run analyses, organize and store data, interface with other systems, automate processing, and more. Some of this code is designed to be reusable as standalone products, or as code in other, larger projects. You can find this code below.

Conservation of inland fish biodivesity

Knowledge of species' spatial distributions is crucial to the identification and prioritization of watersheds in need of restoration.  Coupled with species' status, the presence and or absence of species can indicate biologically diverse vs. depauperate areas. 

Because California inland native fish species have been extensiverly studied (e.g, Moyle 1976, Moyle et al. 1989, Moyle et al. 1995,  Moyle 2002, Moyle et al. 2011, Moyle et al. 2013), changes in species distribution and status can be used as indicators of changes in overall aquatic ecosystem health.  

In this project, we are compiling all available data for California inland native fish species (134) to create current and historical distribution maps using the PISCES database. 

We are also incorporating status scores for most taxon for the years 1976, 2011, and 2013 in order to track changes in species imperilment or preservation.  Because this data is spatially implicit, we will now be able to analyze biodiveristy patterns at multiple scales (statewide, regional, watershed). 

Our goal is to identify areas most likely to protect aquatic biodiveristy into the future as well as areas needing different levels of restoration. 

Future studies will also analyze existing and potential threats to biodiveristy throughout the state, including climate change, dam operations, and extractive landuses. 

The ultimate goal is the prescription of conservation strategies specific to each area.

, , Long-term River Monitoring

The health and function of montane riparian and aquatic ecosystems should be monitored using quantitative, process-based, repeatable metrics in order for resource managers to consistently and affordably maintain, restore and conserve these dynamic environments.  To increase our understanding and better assess the condition of riparian and aquatic ecosystems, we must link metrics of hydrologic alteration with quantitative assessments of physical habitat (geomorphology and water quality) and biotic communities.  The need for water managers to understand these fundamental relationships is particularly acute with climate warming, where temperatures are expected to increase 2 - 6 degrees Celsius.  Anticipated changes to hydroclimate are well documented, and include earlier snowmelt and runoff timing, precipitation shifting from snowfall to rainfall, both prolonged drought and flashier floods, and increased stream temperatures.

Here we build upon six established study sites in the Yuba, American and Tuolumne watersheds to create a long-term monitoring framework that quantifies and evaluates basic stream hydrological conditions and hydrological alteration in an effort to better understand how increasingly scarce water resources affect aquatic ecosystems, and how they can be managed to balance complex ecological and anthropogenic needs.  These long-term study sites are located in streams with varying flow regime types:  unimpaired, semi-impaired (regulated-bypass reaches), and fully impaired (regulated-peaking or regulated-augmented reaches). At each study site, we conduct seasonal surveys to assess current species assemblage and abundance and correlate this information with data on the physical stream conditions including channel morphology, thermal regime, hydrologic variability and habitat availability.  This data also supports monitoring for ongoing modeling studies in the Sierras, including stream temperature modeling at the mesoscale, the effects of hydropower operations on aquatic and riparian ecosystems, and integrating existing understanding of the snowmelt recession limb on stream temperatures and biota.

To learn more visit River Thermohydrographs. This web application uses data collected by the Center for Watershed Sciences at UC Davis as part of long-term Sierra Nevada River monitoring project, building on a previous California Energy Comission Project. Solinst pressure transducers have been deployed (since 2011) in 5 rivers and are logging water temperature and stage at 15 min intervals. Collection of observed data through monitoring is a vital tool for assessing change in aquatic ecosystems, particularly in relation to climate warming and river regulation. This app illustrates a few useful ways to summarize and plot these data. Thermohydrographs are a way to show both stage (level) and water temperature on a single plot.

In addition, check out Time Lapse Hydrography which show time lapse videos about monitoring the Sierra Nevada river's edge habitat with remote game cameras.

, , California Environmental Flows Framework

Flow alterations are a significant driver of species population declines and biodiversity loss in California and globally. When stream flows are altered by human intervention, a wide range of physical and biological processes can be affected, triggering fundamental changes to habitat condition, and the distribution, diversity, and abundance of species. Ensuring the preservation of key flow components can improve riparian and freshwater ecosystem health by restoring physical processes and habitat conditions.

Multiple state and local agencies across California share responsibility for setting flow criteria and prescriptions that protect and improve the ecological health of California’s water resources. These approaches historically have not been coordinated at the statewide level, resulting in fragmented and siloed flow management programs. Consequently:

  • There is no overall framework or guidance for estimating flow criteria,
  • Agencies tend to focus on site-specific solutions, instead of holistically managing the health of California watersheds,
  • Environmental flow data are not readily available or comparable across the state,
  • Improving coordination across California is a challenge,
  • Environmental conditions and pressures vary widely, as do the priorities and capacities of agencies responsible for water resource management.

In 2016, a group of experts self-organized to pool knowledge and data, evaluate methods, and ultimately develop a statewide framework for determining environmental flow criteria for California. The strategy is organized into an approach that varies in scale and detail.

The framework will provide a set of functional flow criteria for all streams in California and a technical guidance document for estimating ecological flow prescriptions.


Process for developing ecological flow criteria and prescriptions in California. CEFF process in green and blue (sections 2 and 3). Orange box indicates additional considerations stakeholders should take outside of the technical process to ultimately arrive at environmental flow objectives (section 4).

Key CEFF products:

  • Reference-based ecological flow criteria: Use the California natural stream classes and the functional flows approach to set flow criteria statewide
    • Statewide applicable method to set flow criteria protective of river-dependent ecosystems
  • Refined ecological flow criteria and ecological flow prescriptions: Provide guidelines for estimating ecological flow prescriptions depending on the regional, local or site-specific context
    • A tailored approach that incorporates specific environmental and water management factors and priorities


The Technical team will continue communicating and collaborating with diverse partners at the state and local level engaged in flow management via the Environmental Flows Workgroup, a sub-group of the California Water Quality Monitoring Council comprised of state and federal agencies with responsibility for environmental flows through their various programs and authorities.