Installation of hydrokinetic power-generating devices is currently being considered for the Yukon and Tanana rivers, two large and glacially turbid rivers in Alaska. We sampled downstream-migrating fish along the margins of both rivers, a middle island in the Yukon River, and mid-channel in the Tanana River in order to assess the temporal and spatial patterns of movement by resident and anadromous fishes and hence the potential for fish interactions with hydrokinetic devices. Results suggest that (1) river margins in the Yukon and Tanana rivers are primarily utilized by resident freshwater species, (2) the mid-channel is utilized by Pacific salmon Oncorhynchus spp. smolts, and (3) only Chum Salmon O. keta smolts utilize both river margin and mid-channel areas. Some species exhibited distinct peaks and trends in downstream migration timing, including Longnose Suckers Catostomus catostomus, whitefishes (Coregoninae), Arctic Grayling Thymallus arcticus, Lake Chub Couesius plumbeus, Chinook Salmon O. tshawytscha, Coho Salmon O. kisutch, and Chum Salmon. Due to their downstream migration behavior, Pacific salmon smolts out-migrating in May–July will have the greatest potential for interactions with hydrokinetic devices installed in mid-channel surface waters of the Yukon and Tanana rivers.