Estuarine beaches are low energy environments found along the coast in several protected places around the world, such as estuaries, bays or areas protected by submerged bars or coral reefs. Although common, these places have been poorly studied. Using a seine net, six beaches were sampled along an environmental gradient for 12 months. During this period, an increase of the dominant species following the increase in salinity and energy values was observed, whilst the opposite pattern occurred for species richness and abundance. Univariate and multivariate analyses showed spatial and temporal variations between beaches and months. Depth and marginal habitats appear to be more important factors than wave height and period, temperature, salinity and pH, which are normally used to describe fish habitat utilization patterns in beaches and estuaries. Nevertheless, specific sampling designs should be proposed to evaluate properly these questions.