Habitat destruction, hydrologic alteration, and nonnative species introductions have greatly altered the composition of North American stream fish assemblages. In the western United States, intermediate-elevation transition-zone stream reaches––those located between higher-elevation mountain and lower-elevation plains areas––historically supported native fish assemblages that included sensitive species and peripheral or isolated populations of more widespread taxa. We compiled historical records and conducted sampling to examine changes to the fish assemblage in the transition-zone reach of South Boulder Creek, Colorado, USA. Because human development of transition zones altered stream and riparian ecosystems prior to sampling, we developed a historical timeline of human activities to formulate hypotheses regarding factors that influenced fish assemblage change through time. Native fish species richness declined by 60% from the likely historical assemblage, and we hypothesize that widespread alteration of stream and riparian habitat in the mid-1800s caused a first wave of species losses, especially taxa with specific habitat or life history requirements. The remaining coolwater native fishes dominated through the mid-1990s, but more recently, the coldwater-tolerant, nonnative Brown Trout Salmo trutta has greatly expanded and is implicated in additional native species loss. Possible management actions to restore native fish assemblages in transition-zone streams include the following: increasing habitat diversity, particularly off-channel backwaters suited to lentic-adapted native fishes; providing refuges from predators or reducing predator abundance; restoring sinuosity to straightened reaches to improve channel function; improving stream connectivity via installation of fish passages; reintroducing beaver or installing beaver dam analogs; provisioning of suitable flow; and eventually, identifying native stocks for reintroduction. Management of other western United States transition-zone stream reaches may benefit from these insights, especially if conservation of the locally distinct native fish assemblages and their scarce habitat is a priority in the face of rapid human population growth and expanding invasive species.