While there is already a comprehensive understanding of the effects of environmental variables, such as dissolved oxygen, temperature and salinity, on the structure, biomass and metabolism of aquatic biota in estuarine habitats, the effect of sedimentation, a harmful underlying factor, remains unclear. The aim of this study was to assess the differences in fish assemblages along the freshwater to salt water gradient of a large tropical estuary, and to evaluate the effects on them of habitat disturbance associated with shallow water sedimentation in the intertidal areas. Fish and environmental variables were recorded in the upper, middle and lower salinity zones of the estuary at ebb tide in both the dry and wet seasons. Sediment samples associated with different levels of habitat disturbance were analysed using granulometry, and their organic content and dissolved oxygen levels were quantified. Water temperature, salinity, pH and dissolved oxygen levels were also measured. Habitat disturbance was found to be correlated with the density, biomass and richness of fish assemblages. A total of 77 species were recorded, forming two distinct fish assemblages, with the Eleotridae family dominating in the upper zone, and Gerreidae, Gobiidae and Tetraodontidae the most common in the middle and lower estuary. Changes in the structure of fish assemblages, including reductions in density, biomass and richness, were associated with disturbance to natural features, where muddy sediment was replaced by sandy sediment and the quantity of organic matter fell. Atherinella brasiliensis was the species which showed a preference for the disturbed areas in the middle and lower zones, while Dormitator maculatus showed a preference for them in the upper estuary. They may be taken as indicators of habitat disturbance due to shallow sedimentation.