Turtle populations are imperiled worldwide, but limited ecological information from unaltered systems hampers science‐based management and conservation of some species, especially riverine turtles such as the spiny softshell (Apalone spinifera). We therefore investigated movements and spatial habitat selection of 54 A. spinifera in 633 river kilometres (rkm) of the least‐altered river in the conterminous United States—the Yellowstone River in Montana—from 2005 to 2009. Movement rates and home ranges were smaller than in fragmented, altered river systems because nesting and overwintering habitats were common and in close proximity. Habitat selection also differed. A. spinifera in the Yellowstone River overwintered in unaltered bluff pools and summered in complex reaches with side channels, islands, and diverse habitats. However, those in the highly altered Missouri River used deep alluvial pools for overwintering and flooded, inundated, or backwatered tributary mouths in spring and summer. Importantly, selected habitats in both rivers were functionally similar, including complex river reaches (with multiple channels, islands, and diverse habitats) and natural pool types. Unfortunately, these are the very habitats that are limited in rivers affected by dams, bank stabilization, and channelization. Therefore, preservation of natural and diverse riverine habitats—and the fluvial dynamics that maintain them—may enhance conservation of A. spinifera in large rivers.