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Projects Worked On

Project Name Description
California Water Myths

In collaboration with the Public Policy Institute of California and other researchers, the Center prepared California Water Myths—a report highlighting eight common water myths, focusing on water supply, ecosystems and legal and governance issues. In providing information to combat these myths, the study establishes a more informed approach to water policy and management in California.

Myths of California Water: Virtual Tour was created as a interactive companion to the California Water Myths report. Experience aerial views of California in locations that relate to the myths and get in-depth information about the realities that combat these myths. The tour also provides links to visual images and further reading.

Shasta River

Interdisciplinary teams of Center scientists are investigating the causes for the decline of salmon and steelhead in Shasta River, historically one of the most productive tributaries in the lower Klamath Basin. A large spring complex (Big Springs Creek) provides the majority of its water, particularly during the summer.

Researchers are developing innovative approaches to restoring and sustainably managing this unique resource for both native fish and for irrigating local ranches and farms.

Though Shasta River provides only 1 percent of the Klamath River’s streamflow, it historically produced 50 percent of the Chinook salmon  -- and it still produces enough fish to support a large proportion of California’s commercial and recreational salmon fishery. Improving freshwater habitat in the Shasta results in disproportionally large benefits for the lower Klamath Basin.

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

El Ocote Reserve

Chiapas (Mexico) and California share many similar challenges regarding the conservation of rivers and streams and the organisms that dwell in them. 

Although fishes in both states are highly diverse, this biodiversity is under multiple threats including effects from cattle grazing, forest fires, dam operations, and climate change.

Collaboration between the El Ocote Biosphere Reserve and the Klamath National Forest began in 1993 in order to provide research expertise and training between the two forests.  Past efforts have documented fish species presence and distribution within the Reserve (2005-2008; Gonzalez-Diaz et al. 2008, Anzueto-Calvo et al. 2013), as well as identified threats to aquatic habitats (2010-2012). 

The University of California, Davis, joined this collaboration in 2013 by providing guidance on extensive water quality sampling and support in continued fish monitoring.  Important water quality parameters (e.g., concentrations of fecal coliform bacteria) were monitored for the first time in 2013. 

Preliminary results suggest that the bacterial content in some surface waters is several 100 times greater than that recommended by Mexican health standards. 

Fishes from several new sites within the reserve were also collected through electrofishing, seining, and gill netting in 2013. 

This information will be used to update management actions within and around the Reserve.  Proposed future efforts include outlining conservation strategies for the Rio La Venta canyon as well as establishing collaborations with other reserves. 

Collaboration with Technische Universität München

Climate change is affecting streams in Bavaria and California in similar ways. 

Water temperatures, extreme flooding events, and the variability of precipitation events are all expected to increase into the next century.  Fishes in streams will have to adapt to increasingly variable environmental conditions. 

Interestingly, both states have several cold-water species, species expected to be the most vulnerable to conditions associated with climate change.  These species include rainbow trout, brook trout, and brown trout. 

Both regions also have salmon, Danube salmon in Bavaria and Ocorhynchus species (e.g., Chinook, coho) in California, and Coregonid (whitefish) species.  However, because the magnitude of effects differ between regions, the response of these species are likely to differ, facilitating the comparison of intra- and interspecies response. 

UCD and the Technische Universität München (TUM) are conducting research to quantify changes in species distributions through the contraction or expansion of ranges. 

The collaborative effort began in 2011 with a two week summer school hosted by TUM.  The main topic of the summer school was Life Sciences in the 21st Century with a Focus on Water.  Later, beginning in April 2012, one of the participants of the summer school, Rebecca Quiñones, was awarded a one-year scholarship to pursue postdoctoral research at TUM. 

During the course of that year Becca collaborated on several research projects that aimed at understanding how landuse practices and resource management interacted with climate change to influence aquatic biodiversity, using fishes as indicator species.  She, along with Drs. Juegen Geist and Karl Auerswald, are currently summarizing the results of a study in the Moosach River in preparation for publication. 

The study looked at how long-term trends in fish abundance may be responding to warming water temperatures and increasing instream channel erosion.  Preliminary results suggest that fish communites are being altered, as a result of declines in gravel-spawning (salmonid) species, due to the aggregation of fine sediment within the stream channel.

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.

Nigiri Project: Growing rice and salmon on a floodway

The Center for Watershed Sciences is investigating harvested rice fields as potential salmon nurseries that could help boost struggling Central Valley populations. Experimental releases of young hatchery salmon on the Yolo Bypass near Sacramento indicate that parts of the 57,000-acre floodway could make productive rearing habitat at relatively little cost to farmers.

Juveniles in flooded rice fields grew much faster and bigger than those released in the Sacramento River. Bigger juveniles survive better when they reach the ocean and are more likely to return as spawning adults.

The Center has been conducting the experiments since 2011 with a consortium of landowners, conservation groups and public agencies. The project takes its name after a Japanese form of sushi that has a slice of fish atop a compressed wedge of vinegared rice.

This UC Davis video, above, shows researchers tagging and releasing juvenile salmon on test fields in February 2013. 

News coverage and commentary:

, , , , , , , , , , , , , Arc of Native Fishes





This study is a unique examination of how local, regional and broad-scale environmental conditions influence fish recruitment, rearing, and reproduction in diverse habitats, including restored wetlands. It will produce essential background information needed to inform how well tidal marsh restoration projects work to support native fish populations in the CLC. We employ an interdisciplinary approach that couples hydrodynamic and particle tracking models with empirical data on distribution and abundance of phytoplankton, zooplankton, epibenthic invertebrates, and juvenile and adult fishes across habitat types. Monthly and continuous data on water quality and flows will be used to inform a developing regional hydrodynamic model which will be implemented. The model will characterize spatial and temporal changes in water quality due to tidal cycles, local inputs and exports. Monthly cruises will collect additional data on water quality, nutrients and chlorophyll-a. Zooplankton and epibenthic invertebrate are sampled by plankton and otter trawls. Fish are sampled using otter trawling, beach seining, and boat electrofishing. All data are collected concurrently to assess prey availability across species’ life histories. Analysis includes hydrodynamic, spatial and statistical approaches.

We are interested in learning how:

1. Increased overland flow and Delta outflow (from precipitation) pushes environmental conditions to favor certain native and pelagic species in the north Delta.

2. Hydrodynamic variability, including spring/neap tide cycles and overland flow, creates conditions that support biomass accumulation and periodic export in terminal sloughs, causing episodic “pulses” of increased food availability to pelagic organisms.

3. Timing of food pulses affects the community composition of fishes by favoring species that are recruiting concurrently with food pulses.

4. Differences in the fish community composition of sloughs is driven by species’ phenology and food web structure.

5. Restoration outcomes for pelagic fishes depend upon the influence of hydrodynamic and geomorphic characteristics on food webs.

For data, contact

, , , Blacklock Restoring Marsh

Historically, the landscape of Suisun Marsh was dominated by tidal wetlands, with vast expanses of marsh plain that would flood during high tides (Moyle et al. 2014). In 1897, construction of a railroad through the western marsh facilitated rapid development of managed wetlands for waterfowl hunting (Arnold 1996). Today, approximately 340 km (210 miles) of constructed levees separate about 210 km2 (52,000 acres) of managed marsh from tidal waterways (Moyle et al. 2014). The Suisun Marsh Habitat Management, Preservation, and Restoration Plan mandates (1) conversion of 20-30 km2 (5,000- 7,000 acres) from managed wetlands to tidal wetlands and (2) the enhancement of 160-200 km2 (40,000- 50,000 acres) of managed wetlands (United States Department of the Interior Bureau of Reclamation 2013). Understanding how managed wetlands influence subtidal waterways is important for water management and the development of restoration designs that will benefit aquatic species. To address this knowledge gap, the UC Davis Blacklock Fish Study was initiated in October 2013 to collect and interpret information on the distribution and abundance of fishes in a restoring tidal marsh, a managed wetland, and adjacent tidal waterways. We used catch per unit effort (CPUE) of fishes collected during monthly trawl and beach-seine sampling conducted by the Blacklock Fish Study to evaluate differences in the distribution and abundance of fishes among a managed wetland, a restoring tidal wetland, and adjacent subtidal sloughs and embayments.

, , , , , , , The Complete Marsh Project


Tidal wetland restoration success in Suisun Marsh requires science-based decision support from gathering and synthesis of pre-restoration baseline data. It also relies on a mechanistic understanding of the influence of hydrogeomorphology (flow, tidal prism, channel structure) on foodweb dynamics. Long term data from that project suggest that tidal wetlands in Suisun Marsh function as nurseries for recruiting juvenile fish, presumably because juvenile fish can utilize both pelagic and benthic food webs during this critical period of growth and survival. This project study mechanisms for creating favorable rearing conditions for juvenile estuarine and migratory fishes that rely on tidal wetlands for food and refuge during this critical period of growth and survival, especially in drought years when suboptimal conditions occur further upstream in the Delta. By modeling food web responses to hydrologic change, and differential resource use among native and alien juvenile fish, we gain a better understanding of how management scenarios can promote fish recruitment. We employ empirically-derived hydrodynamic modeling in conjunction with stable isotope modeling of aquatic food webs and patterns of juvenile fish foraging and growth. We hypothesize that (1) hydrology influences productivity and food availability in tidal wetlands, (2) juvenile fish foraging and growth varies as a function of food availability, and (3) juvenile fish resource use varies as a function of life stage and life history strategy (benthic vs. pelagic). Understanding how tidal wetland food webs support juvenile fish improve designs of tidal wetland restoration projects aiming to increase food availability to juvenile native fishes.

, , , , , , , , , Suisun Marsh Fish Study


The University of California, Davis has been involved in fish and wildlife monitoring and research within Suisun Marsh for 35 years and has been instrumental in detecting important trends associated with naturally fluctuating environmental conditions as well as anthropogenic influences. Research has included a 35+ year time series on the fish and invertebrate communities of the slough networks, research on waterfowl nesting patterns and population biology, and research on the demography of salt marsh harvest mouse. The Suisun Marsh Fish Study anchors this effort as it is the longest established survey in Suisun marsh. It will continue the research of Professor Peter Moyle under the direction of John Durand, and will focus upon the detection of changes in the aquatic ecosystem in response to developing stressors in the San Francisco Estuary (SFE). This time series is designed to further our understanding of the ecology and function of the fish community residing within Suisun Marsh and the San Francisco Estuary (SFE), and acts as one of the key surveys with Interagency Ecological Program’s monitoring effort. Additional tasks will support other research, some of which is ongoing, and some of which is new. Funding for waterfowl studies will support and extend the research of Professor John Eadie, who has studied managed wetland production in Suisun Marsh for the past decade. Funding for mammal studies will support and extend the research of Professor Doug Kelt (UC Davis, Department of Wildlife, Fish and Conservation Biology), who has studied the ecology of saltmarsh harvest mouse in Suisun Marsh for the past 5 years. Funding for herpetological studies will support the research of Professor Brian Todd (UC Davis, Department of Wildlife, Fish and Conservation Biology), who is interested in Suisun Marsh managed wetlands as habitat for western pond turtles. These projects will help to improve management of Suisun Marsh to benefit multiple taxa across changing estuarine conditions. This is particularly important currently because of the effects of drought and climate change, which are likely related to the declines of smelt and salmon in the SFE and its watershed. Trawl catches of native fishes in recent years show less vulnerability in Suisun Marsh to the pelagic organism decline (POD) than in other parts of the SFE. Recent analyses suggest that the Marsh may act as a refuge/nursery for young fishes, buffering stressors that occur in other regions of the SFE. Likewise, Suisun Marsh is a known source of waterfowl production that affects bird populations across the state. The Marsh also functions as a refuge for other taxa, but little is known about these populations. Together, these projects will support an integrative understanding of the ecology of Suisun Marsh and its management practices. The fish study has traditionally been constrained to the slough networks surrounding managed wetlands. Waterfowl studies have focused on pond dynamics. Traditionally, each research domain has not been able to “cross the levees” to integrate their work horizontally across the entire system. However, emerging research supports the idea that certain types of pond management can support both native or desirable fish species and waterfowl. By working with local stakeholders and each other, the UCD research team can examine the effect of changing management strategies in an effort to maximize potential ecosystem benefits, as well as to advise tidal marsh restoration programs.


For volunteer opportunities, contact Teejay O'Rear at