The spatio-temporal structure of the waterbird community on the Mar Menor coastal lagoon (SE Spain) was analyzed in relation to environmental gradients from October 2006–March 2008. Waterbirds were censused at 20 sampling stations according to a zonation scheme based on degree of confinement and primary production, and subsequently modified to match bird use at the landscape level. Multivariate classification and ordination techniques (MDS and SIMPER) identified indicator species and displayed their association with environmental vectors. Abundance of waterbirds increased latitudinally, southward in winter and vice versa in summer. Greater abundance and diversity were found in the southern half of the lagoon in winter, where grebes, gulls and cormorants predominated, and in the northern half in summer, where gulls and terns were dominant. A latitudinal distribution of species was observed; the northern half characterized by Black-headed Gull (Larus ridibundus) and the southern half by Great-crested Grebe (Podiceps cristatus) and Great Cormorant (Phalacrocorax carbo). Such distribution patterns seem to respond to internal functional gradients of the lagoon as well as physical structure of the habitat and human activities. The results show that waterbirds can be incorporated into a monitoring scheme as integrative indicators of spatial gradients of environmental deterioration in the lagoon. In addition, the interpretation of ecological preferences and the response of waterbirds to environmental pressures can serve to assess the conservation status of species at local or regional scales, and act as a warning tool for changes in similar ecosystems.