The main goal of this study was to provide a first approach to the knowledge of the amphibian and reptile ensembles in the flooded savannas of the Pauto River, and to assess the effect derived from the introduction of rice and pasture crops. To do so we first evaluated the richness, abundance, composition and habitat preferences of the species found in the ensemble. We established three factors that determine the ecological dynamics of the ensemble: (1) seasonality, (2) flood pulse and (3) transformations of natural coverts to crops. We concluded that the forest, especially the riparian forest, is the most important natural covert for amphibian and reptile ensembles during the annual climate cycle. Finally, the most harmful and stressful human activity for the flooded savannas of the Pauto River is the practice of transitional crops such as rice.