The aim of this research was to determine the reproductive habitat preferences of several species of amphibians in eastern Spain. We recorded amphibia presence/absence and measured biotic and abiotic variables at 67 ponds in a 43.5 km2 area representing a wide variety of aquatic ecosystems, such as temporary and semipermanent cisterns, drinking troughs, and natural and artificial ponds, all of various sizes and depths. We used this information to predict occupancy using Generalized Linear Models. We built models for the Iberian Ribbed Newt (Pleurodeles waltl), Iberian Green Frog (Pelophylax perezi), Common Midwife Toad (Alytes obstetricans), Natterjack Toad (Epidalea calamita), and Mediterranean Parsley Frog (Pelodytes hespericus). We also found Common Toad (Bufo spinosus) and Spadefoot Toad (Pelobates cultripes) but did not build models for them. The variables that explained occupancy were species specific, with depth and, especially, the type of substratum playing key roles in most of them. Type of substratum reflected pond age and was represented by hard substratum (associated with new artificial ponds and structures), hard substratum covered by soft sediment (associated with old artificial ponds and structures), and soft substratum (associated with old natural ponds). The differences among the species in occupancy models indicate that species-specific management actions may be necessary to preserve the amphibian community in the long term.