The climatic preferences of the species determine to a large extent their response to climate change. Temperature preferences have been shown to play a key role in driving trends in animal populations. However, the relative importance of temperature and precipitation preferences is still poorly understood, particularly in systems where ecological processes are strongly constrained by the amount and timing of rainfall. In this study, we estimated the role played by temperature and precipitation preferences in determining population trends for birds and butterflies in a Mediterranean area. Trends were derived from long-term biodiversity monitoring data and temperature and precipitation preferences were estimated from species distribution data at three different geographical scales. We show that population trends were first and foremost related to precipitation preferences both in birds and in butterflies. Temperature preferences had a weaker effect on population trends, and were significant only in birds. The effect of precipitation on population trends operated in opposite directions in the two groups of species: butterfly species from arid environments and bird species from humid habitats are decreasing most. Our results indicate that, although commonly neglected, water availability is likely an important driver of animal population change in the Mediterranean region, with highly contrasting impacts among taxonomical groups.