Channel morphology, hyporheic exchange, and temperature gradients within Chinook salmon spawning habitat

Snake River fall Chinook salmon (Oncorhynchus tshawytscha ) populations in the Pacific northwestern United States (U.S.) have declined during the past 30 years, leading to their protection under the U.S. Endangered Species Act. Recovery activities and water management planning necessitate an understanding of the physical habitat characteristics affecting Snake River fall Chinook salmon spawning and incubation environments. The purpose of this research was to evaluate the relationships among channel morphology, river discharge, hydrologic exchange, and egg pocket water temperature in Snake River fall Chinook salmon spawning areas. The studies were completed at 15 fall Chinook salmon spawning sites distributed throughout 160 km of the Snake River in Hells Canyon, Idaho, U.S. The results indicate that 84% of fall Chinook salmon spawning areas are correlated with riffles (Chi-square=152.1, df=3, p<0.001), with 63% of those areas located on the upstream side of riffle crests. Differences in head pressure between the river and riverbed were small, often within +/-2 cm. Measured temperature gradients in the riverbed indicated significant interactions between the surface and subsurface water. Neither hydraulic nor temperature gradients at most sites were significantly affected by either short- or long-term changes in discharge operations from Hells Canyon Dam. Only 2 out of 14 study sites exhibited acute flux reversals between the river and riverbed resulting from short-term, large magnitude changes in discharge. At all sites temperature increased with depth into the riverbed, including significant differences (p<0.05) in mean water temperature of up to 3.8°C between the river and the riverbed among all the sites. During each of the three water years studied, river and riverbed temperatures varied significantly among all the study sites, among the study sites within each reach, and between sites located in the two reaches. Considerable variability in riverbed temperatures among the sites resulted in fall Chinook salmon emergence timing estimates that varied by as much as 55 days. By incorporating the knowledge of channel morphology, hydrologic exchange processes and incubation environment characteristics in fall Chinook salmon spawning habitat into recovery activities and water management planning, regional agencies will be better prepared to make science-based water management decisions within the Snake River basin.