Until recently, Camamu Bay (CB), a tropical estuarine ecosystem of the northeast coast of Brazil, state of Bahia, was considered pristine. However, an explosive regional economic growth is increasingly pressuring CB. We used the structure of diatom assemblages to determine whether this economic growth has impacted this habitat. We sampled water and sediment to determine the structure of diatom assemblages and measure physicochemical variables, including nutrients concentrations, salinity, pH, conductivity, temperature, redox potential, suspended particulate matter, dissolved oxygen, and granulometry at each of 30 sampling stations. We produced the percentage of the 11 eutrophication or organic pollution indicator taxa identified (namely Achnanthes fogedii, Bacillaria paxillifera, Cocconeis placentula, Cyclotella striata, Cyclotella stylorum, Halamphora coffeaeformis, Opephora marina, Paralia sulcata var. coronata, Paralia sulcata var. radiata, Planothidium delicatulum, and Tabullaria waernii) for each sample and we also determined the potential correlations of diatom taxa with the physicochemical variables. Our results revealed five distinct diatom groups determined by different combinations of variables reflecting the influence of natural and anthropic factors along the salinity gradient and that salinity exerted the strongest structuring effect on the assemblages. Higher presences of eutrophication indicator species were found near the central areas of the bay and in intermediate areas of Serinhaem and Maraa rivers. Planktonic taxa (e.g., Paralia sulcata) of occurring in the Marau River's indicated high nutrients loading and uncommon hydrodynamic conditions. Our results suggest CB is undergoing a degradation process due to the economic activities. (c) 2022 Elsevier B.V. All rights reserved.