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Projects Worked On

Project Name Description
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.

Big Springs Creek

In 2008, Center researchers seized a rare opportunity to quantify the results of conservation action on a large scale. The Nature Conservancy bought ranchland along Big Springs Creek, a Shasta River tributary that had been degraded by cattle grazing. The conservancy continued ranching but fenced out cattle along the 2.2 mile stream.

Since then, Center researchers and partner Watercourse Engineering, Inc. have been extensively monitoring the creek's recovery, collecting data and analyzing changes in geomorphology, hydrology, hydraulics, water temperature, water quality, aquatic vegetation, aquatic invertebrates, fish assemblage and habitat distribution.

The research:

  • Provides valuable insights to large-scale restoration for salmon.
  • Documents the importance of spring-fed streams as refuges for cold-water fish in a warming climate.
  • Demonstrates how salmon can recover while maintaining a working landscape.
Cosumnes Phase 3

The Center for Watershed Sciences is partnering with The Nature Conservancy in an experimental floodplain restoration on the Cosumnes River. The Center's role in this Department of Fish & Wildlife funded project, "Wildlife And Vegetation Response to Experimental Restoration of Flooded Riparian Forest Habitat for the Cosumnes River Preserve," is intended to conduct biophysical monitoring of an experimental restoration on approximately 800 acres of flooded riparian forest habitat in the Cosumnes River Preserve.

The riparian and floodplain restoration is expected to benefit native fish and wildlife, using natural process restoration techniques where possible and horticultural restoration carried out in an experimental context. This will be one of the first projects to monitor changes in Bay-Delta ecosystem processes resulting from floodplain reconnection.

The project area has been identified as one of the primary locations where riparian restoration can be conducted successfully in the lower Cosumnes River Corridor. 

The Cosumnes Research Group 3 (CRG3) began in the Fall of 2011 to monitor and measure the impact of the planned restoration at the Oneto and Denier Properties along the lower Cosumnes River. The group is currently working on collecting baseline data that will be used to compare with the restored landscape in the following areas: 

  • Groundwater
  • Surface Water
  • Aquatic Ecology
  • Water Quality
  • Soil Carbon
  • Geomorphology
  • Hydrochory
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:

Spring-Fed vs. Snowmelt Rivers: Ecosystem Productivity

This project measures and compares ecological productivity in two types of river systems in the Upper Sacramento River watershed. The project's team of ecologists, geologist and biologists is comparing the food-web dynamics of three spring-fed systems - Hat Creek, Fall River and tributaries of the upper Sacramento River - with those of rivers that receive mainly snowmelt and stormwater runoff in the same watershed.

The study aims to improve understanding of spring systems and their role in sustaining salmonids in California. Spring systems are expected to become increasingly more important for the survival of these and other cold-water fishes as the climate changes and the runoff-fed rivers run low and warm.

Spring rivers are more resilient to long-term warming and changes in precipitation because they receive a constant source of cold water from underground. They often have unique water chemistry that promotes the growth of aquatic plants and insects.

Migration of Fall River rainbow trout

The purpose of this study is to better understand the spawning migration and timing of rainbow trout in the spring-fed Fall River of Northern California.  

The spring water's constant year-round flow and temperature are hypothesized to make for an exceptionally long trout-spawning season – October through June. (Rainbows in the more common snowmelt-fed rivers of the American West spawn only during the spring when flows are suitably high and cold.)

In spring and summer 2013, researchers implanted tags into 500 rainbow trout to track their movement throughout the Fall River watershed. Antenna arrays installed near spawning areas will register when and where the trout go to reproduce. Samples will be taken to see if spawning migration and timing influence the genetic makeup of the fish.

A key question is whether some individual rainbow trout spawn during the same period and in the same places, year after year. If so, special conservation considerations may enter into the management of these populations.

California Trout, the project sponsor, produced this video on the research effort.

, , 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.

Hat Creek Ecological and Geomorphic Assessment

Hat Creek is one of the most famous “spring-river” fly fishing destinations in North America. The lowest 5.5 kilometers of the creek are designated a “Wild Trout Area” (WTA) by the California Department of Fish and Wildlife (CDFW), resulting in management to insure natural reproduction of native fishes. However, since the late 1970’s, declining aquatic habitat quality and resulting fishing opportunities throughout the Hat Creek WTA due to sedimentation issues have prompted assessments of hydrogeomorphic process and conditions in lower Hat Creek, and their possible effects on populations of managed fishes.


Declining fishing conditions through the Hat Creek WTA are largely attributed to segment-scale sedimentation problems and resultant loss of formerly dense beds of aquatic vegetation that provided the dominant structural habitat for aquatic invertebrates and wild trout. Additionally, it is suggested that burrowing muskrats have degraded stream banks, resulting in channel widening and the introduction of additional sediment loads to Hat Creek. The combined losses of aquatic vegetation, channel bed aggradation and channel widening have led to the development of wide and shallow channel reaches with diminished aquatic vegetation cover relative to historical conditions. These aquatic habitats are poorly suited for wild trout, and thus have prompted recent efforts to restore aquatic habitat in select reaches within the WTA.


Through consultation with CDFW, California Trout (Cal Trout) initiated a “pilot” restoration project within the Carbon Reach of the Hat Creek WTA in October 2015. The focus of this pilot project was the introduction of large woody debris (LWD) structures to help stabilize fine sediment, increase spatial variability in flow velocities and depths, and also provide overhead cover to wild trout. Using high-resolution velocity and topographic data collected prior to and following the installation of LWD structures in Hat Creek, the UC Davis Center for Watershed Sciences evaluated hydraulic and geomorphic changes to the Carbon Reach associated with the restoration activities.

Dark Carbon

The floodplains of California’s Central Valley and the tidal wetlands of the Delta have been dramatically reduced in the last 150 years, with both habitats types experiencing approximately a 95% reduction in historic areas.  This fundamental change in habitats has potentially shifted how food webs function in the rivers, floodplains, and tidal wetlands.  We hypothesize that the loss of floodplain and tidal habitats has changed the aquatic food web from a mixed detrital and autochthonous system to primarily an autochthonous system.  This has resulted in a reduced flow of carbon through the food web and thus reduced ecosystem productivity.  

When incorporated into the riverine system, the heterotrophic or detrital based food web may contribute a significant portion of trophic energy to higher-level consumers in floodplains and similar habitats where detrital contributions are large. Previous studies in the California Delta and floodplains have shown that phytoplankton is a significant source of carbon for grazing zooplankton and ultimately higher level consumers. However, these previous studies lacked direct measures of resource utilization by zooplankton in situ and thus our understanding of the detrital food web in the various habitats of the Delta is unresolved. Recent evidence from surrogate floodplains in the Yolo Bypass show that high zooplankton densities and increased juvenile Chinook salmon growth is supported by a heterotrophic food web. It is important to understand the contribution of both the autotrophic and heterotrophic food webs to primary and higher level consumers in floodplains and freshwater tidal habitats to guide restoration and land management actions, and for planning for future climate scenarios.

This project addresses the need for an increased understanding detrital food webs in the North (Yolo Bypass downstream) and Northeast Delta (Cosumnes River and downstream) by use of stable isotope tracers. The use of stable isotopes, Bayesian stream metabolism modeling, and detailed environmental data will offer a high-resolution understanding of carbon flow within and among floodplains and tidal fresh water habitats. Stable isotope tracers will be used to elucidate spatiotemporal food resource utilization by zooplankton and changes in zooplankton community composition in relation to resource changes.

This research will support the priorities of the EcoRestore program where more than 30,000 acres are targeted for restoration into wetland, floodplains and tidal habitats.  A better understanding of the physical processes and resulting food webs within these habitats will allow for better prioritization of restoration locations and expected ecosystem benefits.