The spatio-temporal variability of macro benthic communities was investigated in the 5 main coastal lagoons of Uruguay, and faunal responses to environmental variables were evaluated. This is the first study that addresses spatial and temporal variability simultaneously for benthic subtidal communities of the coastal lagoons in Uruguay. Sampling was conducted in February, May, August, and November 2005, covering 3 spatial scales: lagoons, sites, and replicates. The lagoons were compared through environmental variables, using permutational multivariate analysis of variance and principal coordinates analysis. In addition, distance-based linear model analysis was performed to analyze which environmental variables best determined the macrobenthic community. The benthic community was characterized by a low number of species and high dominance. The most important difference in community structure occurred between Diario, a closed, eutrophic lagoon, and the other lagoons, which are intermittently connected with the ocean. Ocean−land gradients in community structure were observed within all lagoons. Greatest variability in community structure was observed at the largest spatial scale (among lagoons) and at the smallest scale (among replicates). Therefore, both largeand small-scale processes may shape the spatial patterns of these macrobenthic communities. The environmental variables that best explained the macrobenthic community structure were total suspended solids, conductivity, sediment organic matter, phytobenthic chlorophyll a, and macrophyte total biomass. Short-term temporal variability explained a small fraction of the total variation in comparison with spatial variation between lagoons.