Habitat-forming organisms are frequently used as biomonitors in marine environments due to a widespread ability to accumulate toxic contaminants. Few studies, however, have considered the consequences of these accumulated contaminants on the abundant and diverse fauna associated with these habitats. In this review, we summarize research which has investigated the contamination of biogenic habitats (including seagrasses, macroalgae, ascidians, sponges and bivalve reefs) and the impact of this contamination on the habitat use, feeding behaviour and survival of associated epifauna. In many cases, ecological impacts upon epifauna are not simply predicted by levels of contamination in their habitat, but are determined by the foraging, feeding and reproductive behaviours of the inhabiting organisms. Thus, a thorough understanding of these ecological processes is essential in order to understand the effects of contaminants upon epifaunal communities. The scope of biomonitoring studies which assess the contamination of biogenic habitats should be expanded to include an assessment of potential effects upon associated epifauna. When combined with manipulative field experiments such an approach would greatly assist in our understanding of indirect effects of contaminants in these important benthic habitats.