Changes to shallow reef ecosystems are generally mediated by habitat transformation, which has critical implications for ecological communities and food web dynamics, often beginning at basal trophic levels with flow-on effects throughout food webs. Small mobile invertebrates (‘epifauna’) are prolific and ubiquitous on reefs worldwide, representing an essential basal trophic group that fuels much of shallow reef food webs. Epifaunal assemblages were collected across the eastern seaboard of Australia and examined in relation to a diversity of reef habitat types, locations and latitudes, and environmental and ecological gradients. Habitat was the most important correlate of variation in epifaunal assemblages, regardless of latitude or other factors. In a temperate context, macroalgae and turfing algae represented habitat extremes in terms of the size structure and daily productivity of associated epifaunal assemblages. Broad-scale ocean warming and local anthropogenic stressors will likely influence changes to epifaunal assemblages on shallow reefs almost exclusively via transformation of habitats, and the transformation of macroalgae to turfing algae habitat is common on stressed temperate reefs. The consistent trends in epifaunal-habitat associations across large biogeographic scales suggest that accurate prediction of the basal food web resource provided by epifauna is possible when information on habitat distribution is available.