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Arid regions are increasingly being anthropogenically altered. In the north-western Sahara, a growing road network facilitates the use of habitats adjacent to roads. In regions where livestock is the traditional and main economic resource, local people are currently building numerous water cisterns for watering livestock, leading to an increase in the extent of pasturing of domestic livestock. Cisterns may attract desert vertebrates and act as death traps for species with already sparse populations in these arid areas. This paper is the first to examine the impact of cisterns as lethal traps for amphibians and reptiles in the Sahara, using a survey of 823 cisterns in south-western Morocco to identify and quantify species affected. Four amphibians and 35 reptiles were trapped in cisterns, some of which were listed as threatened. At least 459 017 individual amphibians and reptiles were trapped annually within the study area. The low productivity and low population densities of terrestrial vertebrates in this arid region suggest cisterns have a substantial impact upon amphibian and reptile species. As cistern construction is increasing, management actions are required to mitigate this impact on the herpetological community.