We tested for depth-dependent vertical zonation in coral reef community structure with surveys conducted in 2013 at 10 m and 27 m depth off the islands of Moorea, Tahiti, Maiao, and Tetiaroa, which are distributed over ~3500 km2 of the tropical south Pacific. Benthic communities were censused using photoquadrats to obtain percentage cover, first by functional groups (scleractinians, macroalgae, and crustose coralline algae, algal turf, and bare space combined [CTB]), and second by genus for scleractinians and Millepora. Virtually every aspect of community structure differed between the two depths, but the effects were dependent on spatial scale of investigation. Interactive effects of islands and depths determined the abundance of functional groups, as well as seven of eight common coral genera. On the two islands at which two sites were censused, the abundance of functional groups also differed between sites, and was affected by depth × site interactions. The spatially variable effects of depth on community structure underscores the importance of context-specific synergy between biotic and abiotic factors in driving these patterns. Spatial scale-dependent vertical zonation also shows the potential for these effects to be modulated by the changes that have affected coral community structure on contemporary reefs over the last few decades.