The climate in Mediterranean ecosystems is characterised by aestival hot temperatures and water shortages which may affect the behaviour of bats living in these environments. We evaluated the influence of habitat type, habitat structure, and water availability on the foraging behaviour of the Mehely's horseshoe bats (Rhinolophus mehelyi) using classification and regression tree (CART) analysis. Twenty-five individuals were successively radio-tracked during May and June in two colonies (Marias and Aurora) of south-western Spain. Twelve females were tracked in Marias and 13 males in Aurora. Both localities differed in the availability of habitat types: in Marias savannah-like oak woodland dominated the landscape (81% of the study area), whereas in Aurora pasture were dominant (64% of the area). Rhinolophus mehelyi always foraged in woodland; preferentially in cluttered spaces, but also in less-cluttered/more-open ones, while open spaces were completely avoided. Bats foraged close to water bodies, preferentially at distances below 500 m, where they may readily have access to drinking water or may encounter higher insect abundances. The similarity between sexes on the preferences of habitat structure and distance to water suggest that the disparity in the habitat types used by males in Aurora and females in Marias may be due to local availability. Riparian forest is an important habitat for foraging and commuting, and should be scrupulously protected. Conservation strategies should also include the protection of woodland of diverse structure and linear landscape elements. We recommend the creation of water bodies in woodlands to enhance the suitability of foraging sites that might be underused.