Resumo. Abstract Bacterioplankton comprises a highly diverse group of microorganisms, which are dominant in aquatic ecosystems, and play a central role in ecosystem functioning and biogeochemical cycles. Due to their high turnover and dispersal rates, as well as high adaptability and plasticity, microbes are likely to respond quickly to environmental changes and perturbations on their ecosystems. In this opinion paper, we reviewed some studies that addressed bacterial community’s responses to anthropogenic impacts in their aquatic environments. Inorganic nutrients and organic matter inputs from the catchment areas are likely to increase due to changes in climate and land use. These changes will impact the microbial community composition and metabolism, as well the amount of energy and carbon flowing through aquatic food webs as mostly demonstrated in studies from temperate and boreal systems. However, due to the low number of studies on microbial communities in tropical ecosystems, our understanding of how they will respond to perturbations in this distinct environmental context is still limited. Research in microbial ecology in southern countries is still in its infancy and deserves more attention in the future, since tropical aquatic ecosystems are hotspots of biodiversity, host most of the world freshwater reserves, and play a key role in global biogeochemical cycles.