Understanding habitat requirements is vital for developing successful management strategies for threatened species. In this study we analyse the habitat selection of two globally threatened waterbirds (Marbled Teal Marmaronetta angustirostris and White-headed Duck Oxyura leucocephala) coexisting in an internationally important wetland (El Hondo Natural Park, south-eastern Spain) at three spatial scales. We surveyed adults and broods of these species fortnightly during two consecutive years and we related density and presence of birds to several habitat variables. At a pond-selection scale, the density of both species was related to the surface area of the ponds, with Marbled Teal showing avoidance of medium-sized ponds, and White-headed Ducks strong selection for the largest ponds. Within ponds, Marbled Teal avoided open waters, and was mainly associated with Phragmites reedbeds, but also selected areas with saltmarsh and Scirpus vegetation, especially for brood-rearing. White-headed Duck made more use of deeper areas with open water, especially in winter, and Phragmites was the only emergent vegetation with which it associated. When breeding success was very high in 2000, strong creching of broods was observed in White-headed Duck, but not in Marbled Teal. In order to provide suitable habitat for both species, there is a need to maintain spatial diversity with a combination of large wetlands suitable for both species and small, vegetated ones suitable for the Marbled Teal.