Fish habitat quality models (FHQM) developed for rivers consist of relationships between indices of habitat quality and environmental conditions prevailing within sites (local variables). Given the hierarchical structure of these ecosystems, modeling habitat quality over complete rivers may require the inclusion of variables in FHQM that represent the processes operating over a more complete range of spatial scales. The objectives of this study were to quantify the relative importance of local, lateral (characteristics of the shores), and longitudinal (attributes along the upstream–downstream axis of the river) variables on a FHQM developed for parr of Atlantic salmon (Salmo salar). Parr densities (an index of habitat quality) and local, lateral, and longitudinal variables were estimated in 32 reaches of 200 m. FHQM were developed using analytical units (AU) of 50, 100, and 200 m (length of AU in the upstream–downstream axis of the river). The structure and the explanatory power of FHQM were affected by the AU size. In the study river, 98% of the explanatory power of FHQM was imputed to the effect of local variables.