Aquatic organisms respond to the physical environmental across a range of spatial scales, but the precise nature of these relationships is often unclear. In order to forecast ecosystem responses to environmental alterations in watersheds, understanding how processes at different spatial scales affect the ecology of organisms is critical. We used the semi-aquatic American dipper Cinclus mexicanus to evaluate how large-scale, regional variables (e.g. climate); landscape-scale, watershed variables (e.g. land use/cover); and local, reach-level variables (e.g. stream geomorphology) influenced various descriptors of American dipper ecology, including productivity, stable nitrogen isotopes (δ15N), and individual condition. From 2005 to 2008, we collected data at 26 American dipper territories distributed throughout a 25 000 km2 region within Idaho, USA. We then used structural equation modeling to consider potential direct and indirect relationships among scalar factors on measures of American dipper ecology. We found that complex interactions among factors at all three spatial scales influenced dipper productivity, but that δ15N and individual condition were explained by characteristics at the regional and landscape scales only. In particular, model results demonstrate that precipitation was associated with notable variation in multiple dipper responses. Local factors, influencing only dipper productivity, were dominated by hydrogeomorphic characteristics. Our study underscores the simultaneous independent and synergistic roles of environmental factors across spatial scales on American dippers, and offers evidence that pathways influencing aquatic biota may not always conform to hierarchical spatial relationships in watersheds.