Challenges of Juvenile Salmonid Population Monitoring in California's Northern Central Valley

Juvenile passage estimates based on rotary screw trapping are used to evaluate and guide restoration in Battle Creek and Clear Creek in Shasta County, CA.  Restoration includes increased streamflow, dam removal, improving fish passage with screens and ladders, habitat restoration, spawning gravel supplementation and erosion control.  Both creeks have three separate runs of Oncorhynchus tshawytscha with overlapping emergence timing.  Both creeks have populations of resident and anadromous O. mykiss.  Most juveniles are trapped as fry during the winter when high flows, debris, storms, and large catches of vulnerable, listed-salmonids make it difficult to keep traps fishing while minimizing mortality.  Accurately identifying run, anadromy, and life history type requires considerable effort. We are using weirs to separate runs, genetic sampling to verify run designation, otoliths to determine life history and anadromy, and temperature and spawning date to predict emergence timing and development.  Developing juvenile passage estimates with confidence intervals is challenging.  Working with rare fish has prevented estimates of trap efficiency for two runs of Chinook, steelhead, larger fish in general, and fish with alternative juvenile life histories.  Mark-recapture efficiency trials conducted with one size-class of one run of O. tshawytscha are applied towards all other passage estimates. Efficiency trials are also limited by the types of mark we can use, the small and fragile size of the fish, high temperatures when larger fish are migrating and differences in efficiency between hatchery and naturally produced Chinook.  Measuring the effects of stochastic and non-stochastic environmental variability has been difficult.  Missing data during high flows decreases our confidence in passage estimates which are greatly affected by the amount and method of interpolated data.  This poster will present examples of these difficulties and some of our attempted solutions.