Gorgonians are a diverse component of coral reef ecosystems, providing habitats for unique fish and invertebrate assemblages. Evaluating the importance of gorgonians as ecological engineers requires an understanding of their spatial patterns of distribution, abundance and community structure, and the biophysical factors driving them. However, while these drivers have been well-studied for scleractinian corals, they are poorly understood for gorgonians. In this study we quantified the abundance, diversity and structure of gorgonian communities using stereo-video (DOV) transects at three depths (5, 10 and 15m) at 16 locations around the fringing reefs of the Palm Island group, central Great Barrier Reef. The effect of current was assessed by deploying current meters at each location and depth, and spatial heterogeneity in habitat structure by quantifying substratum cover. Gorgonian abundance and diversity increased with depth across all locations, but were weakly positively correlated with current speeds. The structure of gorgonian assemblages varied among depths, with shallow locations dominated by less complex gorgonian structures than deeper ones. Benthic habitat components did not appear to influence gorgonian assemblages, although abundance was low in sand dominated habitats. This study provides a baseline for testing hypotheses about other important factors affecting gorgonian assemblages on other coral reefs.