Coastal marine ecosystems and the habitats within them are among the most productive and ecologically important worldwide. Increasingly, however, coastal ecosystems and their biodiversity are under threat from a variety of anthropogenic activities. As result, knowledge on how nearshore habitats structure fish assemblages is critical to better understand the importance of coastal ecosystems and guide conservation strategies such as Marine Protected Areas (MPAs). In this study, we tested and quantified the influence of habitat classes; rocky reef, seagrass (Posidonia australis) and unvegetated sediment, in explaining the spatial variability in mid-water and demersal fish assemblages. We also assessed the importance of broad-scale seascape patterning of habitats (i.e. composition and area of habitats) on the abundance and diversity of nearshore fishes. Fish assemblages were surveyed using mid-water baited remote underwater video systems (BRUVS) as well as standard BRUVS positioned on the seafloor. Habitat had a significant effect on the demersal fish assemblage with a distinct composition of fishes observed among each habitat. This result was driven by differences in demersal fish diversity and total abundance, where rocky reef harboured a greater richness and abundance of fishes. Several taxa from the demersal assemblage also displayed strong habitat preferences. In contrast, habitat was not an important driver of the mid-water fish assemblage, with inconsistent and highly variable patterns in assemblage structure, abundance and diversity among habitats. Broad-scale seascape patterning also had a pronounced effect on both the demersal and mid-water fish assemblage. Rocky reef habitat connected to large areas of seagrass displayed a higher abundance and diversity of fishes compared to reefs isolated from seagrass. Our findings demonstrate that differences in habitat and seascape patterning are important drivers of the spatial variability observed in coastal temperate fish assemblages. This information could assist the design of MPAs to better represent and protect nearshore temperate biodiversity.