There have been few studies on the structure and dynamics of sponge-dominated assemblages, despite the fact that such assemblages are vulnerable to environmental impacts from many anthropogenic disturbances. Sponges are generally slow to recruit, slow growing and long lived; hence, they may be very vulnerable to anthropogenic and natural disturbances. In order to understand how such assemblages may respond to disturbance, it is essential to measure natural patterns of spatial differences and temporal changes, so that any future impact assessments can be identified. This study quantified and contrasted patterns of abundance in sponge-dominated assemblages on deep reefs (18 to 20 m) exposed to direct oceanic swell with reefs in the more protected entrances to large embayments. We examined the hypothesis that erect sponges would dominate the reefs within embayments, while encrusting species would be more prevalent on the wave-exposed reefs. We also predicted that wave-exposed reefs would show greater temporal and spatial variability. Four reefs within embayments and 4 open coastal reefs, each with 3 nested sites, were sampled with randomly placed photo-quadrats. Sponges dominated the reefs we examined, accounting for around 25% of the cover of the substratum on exposed reefs and usually >40% on sheltered reefs. A total of 82 species of sponge were identified. As predicted, erect sponges accounted for the majority of the species richness and cover of sponges on sheltered reefs, whereas encrusting species predominated on the exposed reefs. The contribution of other sessile invertebrates to the cover and species richness on these reefs was small. nMDS plots revealed striking and consistent differences in the assemblages between the exposed and sheltered reefs, although PERMANOVA failed to detect significant differences. ANOVA revealed significant fluctuations in the cover and richness of taxa at various spatial and temporal scales. Examination of the components of variation of selected taxa showed that most of the variability was found at the smallest spatial scale, i.e. within the residual, and this variability was generally greatest for taxa on exposed reefs compared with sheltered reefs. These results have important implications for monitoring programmes designed to detect environmental impacts on sponge-dominated assemblages.