Application of the Stream Salmonid Simulator (S3) model to assess fall Chinook salmon (Oncorhynchus tshawytscha) production in the American River, California

Executive Summary

Anadromous fish returning to the lower American River are restricted to 36 kilometers of free-flowing river between Nimbus Dam and American River’s confluence with the Sacramento River, California. Salmon in the American River provide an important freshwater recreational fishery. However, annual salmon production in the American River in recent years has been low relative to the mid-1990s (Surface Water Resources, Inc., 2001). To investigate the low production of fall-run Chinook salmon (Oncorhynchus tshawytscha), the Bureau of Reclamation requested that the U.S. Geological Survey apply the Stream Salmonid Simulator (S3) model to the population of fall-run Chinook salmon on the American River.

The American River was chosen among seven candidate Sacramento Basin rivers for S3 application. The American River was selected because of its management and public interest, recently low anadromous fish production, and rich time series of key demographic data needed for S3 application. Data that were not available, however, were empirical estimates on juvenile salmon habitat suitability in the American River. Therefore, a large component of applying S3 to the American River was devoted to the estimation of juvenile salmon habitat suitability and capacity. This entailed snorkeling the lower American River for 3 weeks in March 2021 during the early out-migration period for juvenile Chinook salmon. These efforts were fruitful and showed that the typically small fish ( 0.83), suggesting that fish were feeding at reasonably high proportions relative to the expected maximum consumption as defined by the “Wisconsin” bioenergetics model (Stewart and Ibarra, 1991).

Survival estimates from fry emergence to outmigration at the Sacramento River confluence were generally low when integrated over time. The highest daily survival probability was S_y = 0.93 in 2019, or 50 percent total mortality after 10 days. In contrast, our lowest daily survival probability was S_y = 0.74 in 2015, or 95 percent total mortality after 10 days. Consequently, even our highest estimated daily survival probability might be considered low. This is especially true given that S_y was estimated over a relatively short distance (