Whereas many amphibians use olfactory cues to detect aquatic habitats, less attention has been paid to the specificity of the information carried by these cues with respect to breeding habitat quality. In the present work, we address this question by taking advantage of the selectivity for specific breeding habitats exhibited by the natterjack toad (temporary waters, gravel pits). Toads were sampled from two populations located in semi-arid regions of the Iberic peninsula experiencing Mediterranean climate, and one population in a temperate region of France experiencing oceanic-continental climate. The choice was given in a maze between waters coming either from habitats known to be suitable for the species (temporary waters on an inorganic-dominated substratum) or from unsuitable habitats (ponds with eutrophic water or permanent water on organic-rich substratum). The toads from the temperate region exhibited a clear selection for water from the suitable habitat. In contrast, toads from the Mediterranean region did not show any preference, either when the waters came from their original region or when they came from the other region. These results show that toads can use chemical cues to discriminate specific habitats, allowing them to quickly find suitable habitat patches that are temporary and often spatially unpredictable. Variation between the two populations in the ability to select water quality is likely to be connected with habitat availability at the regional scale.