On tropical reefs where macroalgae are subjected to continuous herbivore pressure, spatial refuges typically are identified as large-scale, landscape interfaces that limit foraging behavior. However, algal distributions and community assemblages may also rely on the availability of smaller scale spatial refuges within the reef. The results of this study demonstrate that the patterns of macroalgal distribution across the back reef of Moorea, French Polynesia, are maintained by herbivores interacting with the small-scale structural complexities of the coral reef landscape. Although the majority of space available for colonization is composed of exposed surfaces, macroalgae rarely are found in the open. Instead, macroalgal occurrence is highest in the protected narrow crevices and hole microhabitats provided by massive Porites spp. coral heads. These distributions are determined initially by post-settlement mortality of young algal recruits in exposed habitats. Rates of consumption for two of the most common macroalgal species found in refuges across the back reef, Halimeda minima and Amansia rhodantha, indicate that algal recruits in exposed habitats are limited by herbivory. While algal abundance and community structure are highly dependent upon herbivore grazing, the availability of small-scale spatial refuges ultimately shapes the distinct community patterns and distributional boundaries of coral reef macroalgae in the back reefs of Moorea.