Biotic indices based on benthic communities have become an important tool in the assessment and monitoring of marine pollution. These communities vary at several spatial and temporal scales giving rise to scale-dependent patterns of distribution, being of particular importance because results from the application of ecological indices, and the subsequent classification of communities, could reflect these variations at several scales. We test some of the most widely applied indices for the evaluation of coastal benthic communities, using a hierarchical spatio-temporal sampling design, within two sets of estuarine habitats in the Atlantic coastal zone of Uruguay. Results showed that ecological indices can vary at different spatial scales, with important variation at small scales. So, independently from the used index, an appropriate sampling design should be taken into account considering different scales (both spatial and temporal). At some of the scales studied, indices appear to reflect natural variations in disturbance through currents rather than variation in anthropogenic effects. At the large scale, variation is low consistent with a preliminary classification of sites according to the putative levels of human activity. The low level of similarity between all indices could be denoting some degree of inconsistency in the assignment of the categories to an ecological status.