The hyporheic environment is composed of a rich meiofauna that depends on water flow, organic matter, and oxygen. The concentration of meiofauna varies spatially (horizontal and vertical) and temporally. Several processes occur at this interface (groundwater and surface water), including biogeochemical processes involving meiofauna. A study of the hyporheic meiofauna community in the sediments of the Beberibe River, in Brazil, was conducted. Meiofauna attained peak densities of 942.8 organisms/10 cm2, with organisms distributed over six taxa, with 98% of them represented by rotifers, nematodes, and annelids. Density was higher in the dry season with an average of 653.1 organisms/10 cm2, and in more superficial sediments with an average of 739.6 organisms/10 cm2. Greater densities were found in coarser sediment with a higher percentage of organic matter. A river bank filtration (RBF) pilot project has been installed, with good results in the attenuation of contaminants and pathogens.