Kokanee, the non-anadromous life history form of Oncorhynchus nerka, use lacustrine habitat in watersheds draining into the north Pacific Ocean. Kokanee have also been widely introduced into reservoirs following impoundment of rivers due to the construction of dams. Locally-adapted subpopulations of Kokanee, however, should be identified and evaluated when implementing watershed-level management strategies. In Chapter 1, I examined fork length, condition factor, and age at maturity for Kokanee in the Williston watershed of northern British Columbia to identify potential spatial and temporal trends in demographic structure following a large-scale stocking program that occurred in the 1990s. Adult spawning Kokanee that were native to the reservoir and collected prior to stocking events were significantly larger and maintained higher condition factors than Kokanee stocked from the Columbia River sampled in any year after 1991. Introduced Kokanee sampled in 2018 and 2019 were the smallest spawners and were significantly smaller than all fish collected between 1989 and 2018; the condition factors of these fish were also significantly lower than native Kokanee and the first spawning cohorts of Columbia-origin fish. The average age at maturity did not change across spatial or temporal scales (3 yrs.). My results indicate an ongoing trend of decreasing spawner size and condition factor for Kokanee in the Williston Reservoir since introduction events in the early 1990s. In Chapter 2, I analyzed the genetic population structure of Kokanee in the Williston watershed, including from the reservoir before stocking Columbia-origin fish and native populations from headwaters of the Williston Reservoir: Thutade, Arctic, and Tacheeda Lakes. Using microsatellite markers, I identified that all fish collected from 2006 to 2019 were introduced Columbia-origin genotypes, and there was no evidence of genetic divergence by spawning location. Native populations in Arctic and Tacheeda Lakes remained entirely separate from the reservoir populations, and there was no indication of past or current introgression with introduced stock. I identified that native Williston Reservoir Kokanee diverged from the Thutade Lake population; as native Williston fish have not been sampled since 2000, it is likely that this population has been extirpated in the reservoir by the successful Columbia-origin lineage. My results highlight an unfortunate consequence of underinformed management practices that failed to recognize the native Williston Kokanee as a distinct population. Strategies that incorporate knowledge of subpopulations of Williston watershed Kokanee, such as genetic populations or reproductive ecotypes, should be prioritized to conserve locally-adapted genetic diversity.