Bat activity and benthic macro invertebrates were sampled at nine paired sites, upstream and downstream from sewage effluent discharges into Irish rivers. Bat activity was measured using broadband acoustic detectors and macroinvertebrates by three 30-s standard benthic kick samples per site. Biological indices of water quality were significantly lower downstream from sewage outfalls, relative to upstream. The soprano pipistrelle (Pipistrellus pygmaeus) was significantly more active (as measured by bat passes per unit time) at downstream sites, while Daubenton's bat (Myotis daubentonii) was less active. These results contrast with those of a similar study in England, where A pygmaeus were less active, and Myotis spp. were more active downstream from sewage outfalls. We suggest that P. pygmaeus were more active downstream in our study because of a preference for preying on small orthocladiinid Chironomidae (non-biting midges), which were significantly more abundant downstream. M. daubentonii may prefer Trichoptera (caddis fly), which were significantly more abundant upstream. Organic pollution may then affect bats, but its effect appears to be more complex than previously implied. Implications of changing nutrient levels in freshwaters for populations of M. daubentonii and P. pygmaeus may be different from what is currently suggested in the literature. (C) 2009 Elsevier Ltd. All rights reserved.