The Chehalis River is a coastal river in southwestern Washington State where decision makers are considering options to reduce flood damage and improve freshwater habitats. This study focused on the mainstem river above and below the location of a potential dam, one of the flood-reduction options being considered. Our objectives were to describe spatial patterns of fish species, physical habitat, and stream temperature, and identify associations between fish species and the physical environment at two spatial scales. Data were collected in spatially continuous reaches following a “riverscape” approach, and patterns in the data were described using three different ordination techniques. Most of the variation in fish species composition occurred at the sub-basin scale (entire study area), with additional but minor patterns at the reach (1-km) scale. At the sub-basin scale, fish species composition was organized in an upstream (salmonid) to downstream (cyprinid) replacement pattern and was best explained by the combination of river location, habitat, and temperature. At the reach scale, physical habitat and stream temperature differentiated juvenile trout versus coho salmon in the salmonid-dominated upstream extent of our study area, and dace versus shiner in the cyprinid-dominated downstream extent. We conclude that salmon and steelhead are particularly vulnerable to habitat loss upstream of the proposed dam because they disproportionately use this area as summer rearing habitat. Protection and restoration of headwater areas, such as our study area in the Chehalis River, will be critical to support salmonid populations into the future.