Many aspects of global ecosystem degradation are well known, but the ecological implications of variation in these effects over scales of kilometers and years have not been widely considered. On tropical coral reefs, kilometer-scale variation in environmental conditions promotes a spatial mosaic of coral communities in which spatial insurance effects could enhance community stability. To evaluate whether these effects are important on coral reefs, we explored variation over 2006-2019 in coral community structure and environmental conditions in Moorea, French Polynesia. We studied coral community structure at a single site with fringing, back reef, and fore reef habitats, and used this system to explore associations among community asynchrony, asynchrony of environmental conditions, and community stability. Coral community structure varied asynchronously among habitats, and variation among habitats in the daily range in seawater temperature suggested it could be a factor contributing to the variation in coral community structure. Wave forced seawater flow connected the habitats and facilitated larval exchange among them, but this effect differed in strength among years, and accentuated periodic connectivity among habitats at 1-7 year intervals. At this site, connected habitats harboring taxonomically similar coral assemblages and exhibiting asynchronous population dynamics can provide insurance against extirpation, and may promote community stability. If these effects apply at larger spatial scale, then among-habitat community asynchrony is likely to play an important role in determining reef-wide coral community resilience.