Fish and Aquatic Ecology

Supporting and maintaining self-sustaining native fish populations.

From declining native fish populations to competing claims for water, water issues affect everyone. Stillwater Sciences specifically tackles issues related to river, estuary, and watershed ecology; most of our projects have the overall objective of restoring and maintaining healthy, sustainable, native fish populations and aquatic ecosystems. This includes:

  • Fish distribution and abundance surveys (snorkel, seine, electrofish, radio tracking, acoustic tracking, trawl)
  • Production estimates (rotary screw trap, fyke net, mark-recapture)
  • Limiting Factors Analyses
  • Habitat use (direct observation, telemetry)
  • Egg and smolt survival (PIT tags, acoustic tagging, artificial redds)
  • Aquatic food web (gut content analysis, stable carbon and nitrogen isotope analysis)
  • Multi-stage stock-production models
  • Habitat/life-stage based models
  • Rapid bioassessment protocols (EPA-EMAP, SWAMP, CSBP)
  • Instream flow/habitat assessment (IFIM, PHABSIM)
  • Criteria-based instream habitat mapping using Low Elevation Aerial Photography (LEAP)

In addition to our comprehensive understanding of fish ecology, we also focus on how aquatic organisms interact with their physical environment by examining the linkages between habitat structure and the physical processes shaping this habitat. This approach allows us to provide sound solutions to complicated aquatic management problems, including challenges related to climate change, and to develop effective management strategies at scales ranging from small urban streams to large valley watersheds and deltas.

Stillwater Sciences holds a NMFS Section 10(a)(1)(A) permit authorizing take of ESA-listed Southern Oregon/Northern California Coast coho salmon, Central  California Coast coho salmon, California Coastal Chinook salmon, Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, Northern California steelhead, Central California Coast steelhead, Central Valley steelhead, South-central California Coast steelhead, and Southern California steelhead associated with various Bay Area, Central Valley, and southern California coastal watersheds. Stillwater biologists also hold a USFWS Section 10(a)(1)(A) permit authorizing take of ESA-listed tidewater goby.


Our work includes field-based sampling of aquatic habitats and the species found there, as well as fish population modeling, diet tracking, and food web analysis.

Download an overview of our fish and aquatic ecology services [pdf, 2.6M]


Ethan Bell
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Use of streambed substrate as refuge by steelhead or rainbow trout Oncorhynchus mykiss during simulated freshets

A flume was used to estimate the carrying capacity of streambed substrates for juvenile steelhead or rainbow trout Oncorhynchus mykiss seeking refuge from freshets. The simulated freshets had mean water column velocities of about 1·1 m s-1. The number of fish finding cover within the interstices of the substrate was documented for different substrate sizes and levels of embeddedness. The availability of suitable refuges determined the carrying capacity of the substrate for O. mykiss. For the size of the fish tested (122 mm ± 13 mm S.D.), the number of interstices with depths ≥ 200 mm measured with a 14 mm diameter flexible plastic tube was the best predictor of the number of O. mykiss able to find cover (R2 = 0·75). Oncorhynchus mykiss seeking refuge from freshets may need deeper interstices than those seeking concealment at fall or winter base flows. The availability of interstices suitable as refuge from high flows may determine fall and winter carrying capacity. Watch the video here.

Contact: Frank Ligon
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Diverse methods, robust results

Site-specific habitat conditions—including abundance of prey, predators, and cover/habitat—naturally affect fish behavior, distribution, and density in any given reach. To increase confidence in the results of our fish sampling efforts, we compare results generated by different sampling methods such as electrofishing, daytime snorkel surveys, and nighttime snorkel surveys. On Rock Creek, OR and the McCloud River, CA, we have initiated nighttime snorkel surveys in many of our long-term projects. This diversity of approaches helps ensure that the most scientifically robust results are used in analyzing population dynamics.