California Freshwater Fish Laboratory
University of California
California Freshwater Fish Laboratory

Research Projects

Choose a project to get more information and links to publications.

California Fish Phone App

Rainbow trout, Deer Creek, CA, 2007. Photo by Dave (Gio) Giordano.
California naturalists and anglers often observe fish in streams and lakes but may not be able to identify them to the species level.  Furthermore, access to a computer with an internet connection may be difficult in the outdoors, but a growing number of people now have access to a smartphone.

Clear Lake Information Public Online Database

Clear Lake shoreline. Sept. 24, 2007. Photo by Lisa Thompson
Clear Lake is the largest natural lake wholly within the boundaries of California and is a valued resource for residents of local communities and holiday tourists. The lake also supports a lucrative sportfishing industry that is very important to the economy of Lake County. Management of water quality in the lake is particularly challenging. The summer reaction of the lake, including overgrowth of noxious weeds, and blooms of true alga and blue-green algae, results in negative economic impacts and public perceptions.

Modeling Tool to Assess and Mitigate the Effects of Small Hydropower on Stream Fishes in a Changing California Climate

Kilarc Power House on Cow Creek, CA, August 3, 2007. Photo by Lisa Thompson.
California’s 2005 Energy Policy Act (EPAct) provides incentives for new hydropower development that could be used to encourage development of additional hydropower capacity in California. Meanwhile, California’s mandate to increase the contribution of renewable energy sources and reduce greenhouse gas emissions has led to incentives to increase the production of energy from small hydropower as part of California’s Renewable Portfolio Standard.  However, this may come with costs to native fish species.

Temperature Preference and Tolerance of Hardhead Minnows

Dam on South Fork American River, April 21, 2010. Photo by Lisa Thompson.
 California’s populations of hardhead minnow (Mylopharodon conocephalus), a fish species of special concern, have experienced population declines, possibly due to habitat perturbations, including dam construction with consequent temperature changes and the introduction of non-native species to California’s mid- to low-elevation streams. Environmental temperature effects on this large (up to 60 cm (2 ft) Standard Length) native species are poorly documented.

Climate Change and Spring-Run Chinook Salmon

Butte Creek, CA, July 7, 2009. Photo by Lisa Thompson.
Spring-run Chinook salmon (Oncorhynchus tshawytscha) are vulnerable to climate change because adults over-summer in freshwater streams before spawning in autumn. In California’s Central Valley their distribution is limited to three watersheds with small numbers appearing intermittently in seven other watersheds where access to coldwater pools remains unobstructed. Annual spring-run Chinook salmon runs used to number approximately 1 million fish, but they have declined to approximately 16,000 in the Central Valley.

Hydropower-related pulsed-flow impacts on stream fishes

Pulsed flow release from Camino Dam, Silver Creek, CA. Sept. 15, 2005. Photo by Lisa Thompson.
The societal benefits of hydropower systems (e.g., relatively clean electrical power, water supply, flood control, and recreation) come with a cost to native stream fishes. Until now, the specific effects of the associated pulsed-flow releases on stream fishes have not been reviewed in detail, or synthesized in a conceptual model that would allow managers to predict and mitigate the negative effects.

Steelhead Distribution and Habitat Use in the Salinas River Watershed

Juvenile southern steelhead trout, in Salinas River tributary. Photo by Jenna Voss.
The Salinas River and its tributaries have been designated by the National Marine Fisheries Service as critical habitat for steelhead (Oncorhynchus mykiss), listed as “threatened” under the Federal Endangered Species Act. The watershed is part of the South-Central California Coast Evolutionarily Significant Unit (ESU) for steelhead. Large wood is known to be very important to fish habitat in conifer-dominated streams of the Pacific Northwest, but has not been well studied in hardwood-dominated streams of the central California coast.

Effects of Pulsed Flows from Dams on Fishes: Field and Lab Studies

Silver Creek, CA, during pulsed flow release on Sept. 15, 2004.
Pulsed flows in rivers are relatively rapid increases in flows followed by relatively rapid decreases, with flow fluctuations lasting minutes, hours, or days. Reasons for pulsed flows include: generating electricity, flushing streambeds, facilitating human recreation, providing additional water for downstream diversion for irrigation, and preventing reservoirs from flooding. Although pulsed water releases provide obvious benefits to humans, the cumulative effects of repeated and unseasonal flow pulses on aquatic communities are relatively unknown.

Restoration of Wild Eagle Lake Rainbow Trout

Pine Creek rainbow in upper watershed, 2007
Pine Creek historically provided critical spawning and rearing habitat for Eagle Lake rainbow trout. Over the past 100+ years modifications of Pine Creek watershed decoupled the trout from its stream habitat. After 20+ years of restoration efforts in the Pine Creek watershed, a key question is, are rainbow trout able to migrate to the headwaters of Pine Creek?

Management of Leonard Lake

Leonard Lake, CA. Photo by Lisa Thompson.
Leonard Lake is the largest natural lake in Mendocino County, and is located approximately 140 miles north of San Francisco, California. The managers of the lake are interested in the current state of the lake, and in managing it sustainably for future generations.

Rainbow Trout Distribution and Habitat Use in Rangeland Streams

Cattle in pasture near Cow Creek, 2004. Photo by Lisa Thompson.
Many California rangeland watersheds experience extensive livestock use, and many landowners divert stream water for pasture irrigation. Fish population declines and habitat alteration across northern California watersheds have resulted in the listing of species under the Endangered Species Act, and the implementation of water quality strategies for impaired waterbodies. These events highlight the importance of species recovery and habitat restoration efforts, and bring the potential impacts of agricultural practices under increasing scrutiny.

Conservation of Shasta River Coho Salmon

Shasta River and Mount Shasta, Dec. 1, 2004. Photo by Lisa Thompson.
Coho salmon (Oncorhynchus kisutch) in the Shasta River are part of the federal Southern Oregon/Northern California evolutionarily significant unit (SONC ESU) and are listed as threatened. At the state level coho salmon in the Shasta River are part of the Northern California designation, and are also listed as threatened. There are multiple factors that may limit salmonid populations in the watershed, including water quantity, water quality, riparian habitat quality, excessive sediment yield, spawning requirements, and rearing requirements.

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