Investigating how Mediterranean wetlands respond to adjacent land use conversion, is an important first step in mitigating the impact of human encroachment and other environmental stressors. We monitored the composition and structure of waterbird assemblages, in a Mediterranean urban marsh, subjected to severe anthropogenic pressures. Remote sensing indicated that in the last two decades Boussedra Pond was subjected to landfill, resulting in a substantial reduction (~ 50%) of the marsh, while due to a lack of urban planning urban built-up and agriculture areas expanded considerably in its surroundings. Seasonal changes in the diversity of waterbirds, including the globally Endangered (EN) White-headed Duck Oxyura leucocephala and the Near-Threatened (NT) Ferruginous Duck Aythya nyroca, reflected the importance of the site as a staging and wintering area for many migratory species. The long-term study also suggested that breeding waterbirds species respond differentially to the loss and degradation of habitats, as highlighted by the resilience of the synanthropic Moorhen Gallinula chloropus and the disappearance of several breeding marsh specialists, like the Little Bittern Ixobrychus minutus and the Western Marsh Harrier Circus aeruginosus. The study points out the need for both a coordinated cross-sectorial land use planning and an immediate, affordable and sustainable wetland conservation action.