Despite knowing that agricultural practices affect river ecosystems, studies on water quality and associated hyporheic invertebrate communities are rare. Yet such knowledge is essential for sustainable use of agricultural and water resources. This study, carried out in the agricultural region of south-eastern Ireland in Spring 2007, examined the effect of water pollution on hyporheic fauna. Six river sites of known water quality were assigned to two treatments, namely, clean and polluted rivers. Two hyporheic habitats, below the wetted channel (hyporheic substream) and below the exposed gravel bank (parafluvial), were sampled within each treatment. Total invertebrate densities and richness, crustacean densities and richness, and densities of Ephemeroptera, Plecoptera and Trichoptera (EPT) were significantly reduced in polluted hyporheic and parafluvial habitats. A higher recorded concentration of nitrate in the polluted hyporheic substream habitats was a significant factor in determining the invertebrate assemblages, with reductions in total and crustacean densities, and EPT richness. Similarly, invertebrate density and richness were reduced in polluted parafluvial habitats, likely being related to agricultural intensity, management practices and reduced riparian buffering. This study highlights the direct effects of agricultural practices on the invertebrate communities of hyporheic habitats and emphasises the need for holistic management and conservation measures to ensure future protection.