Knowledge about the hyporheic zone is important to understand the pollutant attenuation processes that occur during the aquifer recharge, whether by natural or artificial means, for example, Bank Filtration. In this paper, the structure of the hyporheic meiofauna and the influence of pollution, microphytobenthos and sedimentological parameters (grain size, organic matter and CaCO 3 content) were studied at a periurban area of Beberibe River (Northeastern Brazil), the location of a riverbank filtration (RBF) pilot project. PERMANOVA analysis indicated interactions between meiofauna community and the sampling sites, rainfall seasons, and depth. The release of untreated wastewater was the most influential factor for physical and biochemical features of the hyporheic zone, since the sampling sites with higher levels of elements related to eutrophication supported the highest levels of meiofauna abundance, fine sediments, organic matter, and CaCO 3 content. It was verified that organic matter from domestic wastewater in tropical streams can promote protective effects that favor the retention and biodegradation of pollutants in the hyporheic zone. The results reveal that, even in eutrophic rivers, there are factors that contribute to the processes of pollutant attenuation in tropical hyporheic environments. The results demonstrate the potential for using RBF in communities without adequate sanitation, especially in developing countries.