A range of physical and biological factors influence species distributions and community structure in marine ecosystems. Benthic assemblages on subtidal rocky reefs in southwestern Australia are characterized by a high diversity and coverage of macroalgae and a relatively low abundance and diversity of large, conspicuous invertebrate herbivores. Here, we examined distribution patterns of key benthic organisms (sea urchins, predominantly Heliocidaris erythrogramma, and the canopy-forming macroalgae Ecklonia radiata and Sargassum spp.) and related these patterns to a suite of environmental variables, including geological measures, at 20 sites distributed across 5 rocky reef locations off Perth, Western Australia (WA). Abundance patterns varied at multiple spatial scales and no clear relationship between the abundance of sea urchins and the cover of large macroalgae was observed. The abundance of sea urchins was negatively related to 'substrate cohesion strength' (a measure of limestone reef integrity), which was positively correlated with the percentage cover of E. radiata. The cover of Sargassum spp. was negatively related to fetch. Our results indicate that the distributions of key benthic organisms in temperate WA exhibit considerable spatial variability that appear to be largely driven by physical habitat structure and bottom-up factors rather than through any trophic interactions. © 2014 Taylor & Francis.