Background. Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout. Methods. Between 2008 and 2013, 88 large (≥ 500 mm) Bull Trout and 149 large (≥ 500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake. The subsequent detections and angler recaptures were analysed using a Bayesian individual state-space Cormack-Jolly-Seber (CJS) survival model with indicator variable selection. Results. The final CJS survival model estimated that the annual interval probability of being recaptured by an angler was 0.17 (95% CRI 0.11 - 0.23) for Bull Trout and 0.14 (95% CRI 0.09 - 0.19) for Rainbow Trout. The annual interval survival probability for Bull Trout was estimated to have declined from 0.91 (95% CRI 0.77 - 0.97) in 2009 to just 0.45 (95% CRI 0.24 - 0.73) in 2013. Rainbow Trout survival was most strongly affected by spawning. The annual interval survival probability was 0.77 (95% CRI 0.68 - 0.85) for a non-spawning Rainbow Trout compared to 0.42 (95% CRI 0.31 - 0.54) for a spawner. The probability of spawning increased with the fork length for both species and decreased over the course of the study for Rainbow Trout. Discussion. Fishing mortality was relatively low and constant while natural mortality was relatively high and variable. The results are consistent with Kokanee abundance as opposed to angler effort as the primary driver of short-term population fluctations in Rainbow Trout abundance. Multi-species stock assessment models need to account for the fact that large Bull Trout are more abundant than large Rainbow Trout in Kootenay Lake.