Human communities often discharge wastewaters into estuaries, influencing their organic and pollutant loading, benthic community and trophic structure. The implementation of the Water Framework Directive has encouraged the treatment of wastewater discharges across European estuaries, but the implications for invertebrate and waterbird communities are poorly understood. We explore the effects of untreated sewage discharges on the distribution and abundance of foraging black-tailed godwits Limosa limosa and their main benthic prey (bivalves and polychaetes) on the Tejo estuary in Portugal, a major European Special Protection Area with ongoing wastewater improvements. Patches of mudflat in close proximity to sewage streams (<30 m) can support polychaete densities and biomass that are an order of magnitude higher than more distant sites (>70 m), and godwits foraging in these areas can attain the highest intake rates recorded for the estuary. However, high intake rates can also be attained on bivalve prey, and bivalve biomass and density increase slightly with distance from sewage streams. As the organic input from sewage outfalls influences invertebrate abundance and godwit foraging rates over relatively small areas, the ongoing implementation of a sewage treatment network on the Tejo estuary seems likely to have only a limited impact on the wintering godwit population. The localized effect of untreated sewage discharges on benthic communities suggests that the implications for predatory birds are relatively minor where alternative prey are available, but may be more severe in locations with more depauperate, polychaete-dominated invertebrate communities.