Ten shallow (<20 m) reefs at Naval Station Guantánamo Bay, southeastern Cuba, were surveyed during July–August 1996 to evaluate topographic complexity and community structure with respect to depth-related zonation and potential sedimentation impacts from the Guantánamo River. While the methods employed were not novel, coral reefs in the study area had not been previously studied and, because of low human population density, may provide useful comparisons to more disturbed reefs in the Caribbean. On leeward and windward sides of the Bay, four shallow (5 m) and four deeper (10 m) spur-and-groove reefs were surveyed, along with two reefs within the mouth of the Bay. On each reef, four 25-m transects were oriented perpendicular to shore on four haphazardly selected spurs and used to randomly select 1 m × 1 m quadrat locations. Benthic coverage using point-intercept counts and topographic complexity using the chain-length method were quantified within quadrats. All sampled reefs were dominated by algae, especially algal turfs, and stony corals. Mean percent algal cover among reefs ranged from 50 to 78%, while coral cover ranged from 11 to 49%. Analysis of variance showed that depth was more important than location in explaining the variability in mean coral cover. Cluster analysis using percent coverage of all bottom types and relative coral cover confirmed that reefs at the same depth were more similar in benthic composition. Several species considered to be less tolerant of sedimentation, however, were more abundant on windward reefs, suggesting that differences in sedimentation between windward and leeward areas may affect relative species abundance, but not total coral cover. Percent coral cover estimates from 9 of the surveyed reefs were well above recent values reported for other wider Caribbean reefs. The predominance of corals on these reefs is surprising, given the low abundance of herbivores (due to mass mortality and overfishing) and possible disease outbreaks affecting acroporid corals. These disturbances appear to have had less severe consequences than for other wider Caribbean reefs such as those in Jamaica and the Lesser Antilles, potentially due to the relative rarity of destructive storm events.