Run timing and spatial locations of spawning habitats are often used to identify stocks for conservation planning or management of salmonid fishes. Although complex stock structure is most common within large watersheds with diverse habitats, even small drainages can produce multiple co-occurring spatially or temporally isolated populations or “stocks.” This project sought to address the potential existence of stock structure of Coho Salmon Oncorhynchus kisutch in a small coastal watershed on Kodiak, Alaska that supports vital subsistence and recreational fisheries and is currently managed as a single stock. We radio-tagged a total of 348 adult Coho Salmon upon freshwater entry into the Buskin River across three spawning seasons (2015–2017) and tracked in-river movements to the final locations where mortality signals were recorded. We identified two primary spawning habitats within the system: main-stem and lake tributaries, with 54% (range of 47% to 61%) of tagged fish with determined fates tracked to main-stem river spawning areas and 46% (range 39% to 53%) presumably spawning in small tributaries of the 1-km² Buskin Lake at the headwater of the watershed. Despite distinct spatial differences in spawning locations, main-stem and tributary spawners did not differ in migration timing into freshwater (difference in run timing of main-stem versus tributary spawners = 1 d) nor body size (main-stem mean body length, mideye to tail fork = 625 mm, tributary mean = 613 mm). Unexpectedly, we determined nearly 70% of all Coho Salmon spent at least some time in Buskin Lake, including 54% of main-stem spawners, suggesting a potential role of Buskin Lake as an important staging habitat for premature migrating adult Coho Salmon who enter freshwater in advance of final maturation. We also identified areas consistently used for holding prior to spawning that could be used in spatial management planning and during times of necessary conservation to ensure integrity of the stock for the future.