The stable flow and temperature regimes of spring-fed streams are expected to provide unique foraging habitats and thermal refuges for fishes, but little is known about the seasonal utilization of spring-fed streams by fishes. Here, we investigated the seasonal changes in population density and stomach contents of juvenile Oncorhynchus masou masou in adjacent clastic lowland spring-fed and runoff tributaries in northern Japan. The results suggested two ecosystem functions of spring-fed streams. First, the stable flow regime of spring-fed streams can create depositional habitats and harbor abundant detritivores, and these macroinvertebrates, in turn, provide a significant food resource for juvenile fishes. Second, the stable temperature regime of spring-fed streams provides thermal refuges during hot and cold weather. Thus, the cooler spring-fed tributary abundant in aquatic prey forms a peak of juveniles' population density in August (1.3 individuals/m²). In November, the juvenile population increased four-fold (5.2 individuals/m²), perhaps affected by the warm environment of the spring-fed tributary. The abundance of eggs spawned by both wild and hatchery-reared O. keta may have also contributed to this increase in population through the provision of a nutritious food resource. We concluded that two ecosystem functions were identified in spring-fed streams in the summer, but additional investigation is required to examine the ecosystem functions in winter. Nevertheless, the results highlight that the heterogeneous environment formed by spring and runoff waters may strongly influence the spatiotemporal predator–prey interactions in river networks.