Seagrass meadows provide a spectrum of anthropogenically important ecological functions. However, these ecosystems are globally declining under human influence. Submerged communities inhabiting different water motion regimes are experiencing different stressors and are likely to respond differently to climate change. This study couples a comparison of conditions between water motion regimes with indications of susceptibility to stochastic disturbances and investigates both their influences on seagrass meadow community structure. Community surveys were conducted in a semi-structured manner at three different wave-exposed sites on Saint Martin, French West Indies. Measurements of mass transfer and other abiotic features were taken alongside. Nutrients, pH, salinity, light, temperature and DIC could not explain dissimilarities in macrophyte communities between sites. Multivariate ordination methods in which the bareness of the seafloor was used as a gradient, gave indications of setbacks to earlier successional stages in seagrass meadow communities. Indirect assessments of grazing pressure yielded sea urchins as potential herbivores in studied meadows, having a possibly profound effect on altering species composition, but probably having no effect on sea floor cover. The wave-exposed community showed more bareness in between macrophytes. Exposed sites, which are prone to experience higher rates of stochastic disturbances, probably need calcifying algae to stabilize sediment for recolonization after meadow losses. Penicillus capitatus and Halimeda spp., both rhizophytic calcifying algae, were found to be the most probable colonizers of bare seafloor. The role of these species as supposed colonizer, and therefore establisher or facilitator of seagrass meadows should be experimentally investigated, as these algae are thought to suffer competitive disadvantages under future ocean acidification scenarios.