Habitat use of a species is a vital component in explaining the dynamics of natural populations. For mobile marine species such as fishes, describing habitat heterogeneity at a seascape scale is essential because it quantifies the spatial extent to which fishes are interacting with their environment. Here, we explored the relationships between habitat metrics and the density and size of coastal rocky reef fishes across a seascape that is naturally fragmented. Multibeam sonar and GIS analysis were employed to create a seascape map that explicitly depicted bathymetry and spatial configuration of rocky reefs in southern California. Georeferenced subtidal transect surveys were conducted across this seascape to describe habitat attributes, including the density of macroalgae, and record the number and size of fishes. To compare the relative influence of habitat metrics, individual variables were grouped into macroalgae, bathymetry, and spatial configuration components, allowing for comparisons of within-patch to surrounding habitat metrics in describing the numerical density, biomass density, average size, and maximum size of five abundant rocky reef fishes. We found that responses to different habitat components were dependent on particular species, the choice of spatial scale, and the inherent characteristics of the seascape itself. Notably, the relative influence of seascape components were dependent on the configuration of the seascape; where fishes in a more isolated and less-connected seascape were more influenced by spatial configuration than a seascape with greater habitat connectedness. This study demonstrates that explicit habitat maps allow for a more comprehensive understanding of population structure when describing fishes across large spatial scales.