We describe the spatial and temporal variation in the main characteristics of amphibian breeding habitats in Doñana National Park (south of Spain), during two hydrologic cycles with different rainfall amounts and timing (2002–2003 and 2005–2006). We also evaluate amphibian habitat requirements following a model selection approach based on Akaike’s Information Criterion. Our results evidenced large spatial variability in all pond characteristics and inter-annual differences in pond hydroperiod, depth, and most water-chemistry characteristics. We observed a remarkable independence of pond characteristics at different sampling dates, suggesting that a pond description based on a single survey may not be representative. Eight of nine amphibian species attempted breeding in both years in spite of the marked inter-annual variability. Habitat models were species-specific and year-specific, as we found inter-annual differences in the pond characteristics relevant for species richness or for the relative abundance of particular species. All these results suggest that this large and diverse network of ponds provides different habitat opportunities each year, favouring the long-term persistence of the whole amphibian community.