Urban areas are increasingly occupying the margins of estuarine wetlands. Consequently, it becomes important to understand how the presence of these urban areas influences the use of adjacent intertidal habitats by waterbirds. Wintering waterbirds were regularly counted on 28 mudflat sectors along the northern margin of the river Tagus estuary, Portugal, which includes large urbanized extensions. Sectors were characterized using 16 variables related to its physical characteristics and human influence and related to bird density and diversity using multiple linear regression. Species richness was positively influenced by wider mudflats and a margin covered with saltmarsh. The individual response of seven of the most abundant bird species to these variables differed between species, but the abundance of half of these species was significantly influenced by variables potentially related to the presence of urban areas.