Abstract The Mar Menor, a 135-km2 saline lake, is the largest water surface on the western Mediterranean coast, and an internationally important bird area. It is surrounded by a large irrigated agricultural plain, with dense tourism developments. Although the impacts of these activities on water quality are locally evident, their effects on waterbird populations are poorly known. In the winter 2004–2005, we studied the distribution of four waterbird species (Podiceps cristatus, Podiceps nigricollis, Phalacrocorax carbo and Fulica atra) around the main drainage channel that discharges into the lake, where it was feasible to infer spatial patterns of eutrophication (alongshore and shore centre) from previous environmental surveys. Waterbirds were counted along a stretch of undeveloped shoreline extending southwards from the channel outlet, in contiguous sections, and in bands parallel to the shoreline. Linear mixed models (LMM) indicated the population density increased only markedly for grebes (Podiceps cristatus, Podiceps nigricollis) and coot (Fulica atra) in littoral bands qualifying as eutrophic, but not an alongshore response, with their finescale alongshore distribution being apparently unrelated to nutrient sources. Considering the whole lake, however, the temporal trends and distribution of the wintering populations indicated that waterbirds respond numerically, in a guild-specific way, to nutrient inputs. Grebes and coot could be a useful ‘two-stage’ warning signal for potential problem areas affected by similar influences.