Co-existence of species has been a central debate in ecology for decades but the mechanisms that allow co-existence are still heatedly disputed. The main paradigms have shifted among the importance of competition, predation and abiotic conditions as determinants of community structure. Differential habitat selection is considered to reduce competition and hence allow co-existence. Our goal was to test hypotheses regarding how breeding site use of a population that was patchily distributed on a dynamic floodplain may facilitate coexistence: 1) do species co-occur randomly or do they occur more or less often than expected by chance? 2) Do species use the same habitat types in equal proportions or do they use them differentially? 3) If they use habitat types differentially, is this differential use related to abiotic and biotic conditions? 4) Does interspecific competition predict breeding site use or do abiotic conditions and predation risk better predict habitat use? We collected presence/absence (i.e. detection/nondetection) data of egg clutches and larvae of four pond-breeding anuran species during a two year study at a total of 353 ponds. We used site occupancy models and model averaging techniques to predict breeding site selection in relation to habitat types, abiotic and biotic factors. These parameters were corrected for imperfect detection of species. The rates of co-occurrence were consistently higher than expected by chance. Species differed in the use of the main habitat types. Habitat types that were used by multiple species were used in a species-specific manner in relation to both abiotic conditions and predation risk. Species preferred ponds where other species and fish were present. Although niche differentiation in breeding site selection is evident, our results do not support the pervasive role of competition avoidance in governing current breeding site selection. We conclude that differential habitat use and differences in response to abiotic conditions and predation risk can override competitive interactions, thereby facilitating local co-existence and high species diversity.