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The dataset contains 708 records of 13 amphibian and 13 reptile species recorded in the lower reaches of the Sabor River (NE Portugal), and that were included in the baseline studies to define biodiversity offsets of the Baixo Sabor Hydroelectric Dam, promoted by EDP – Energias de Portugal, S.A.. Data was collected between March and November 2009, during thirty five (n=35) days/nights of field sampling carried out in the area to be flooded by the two reservoirs, and within a 5-km buffer around each reservoir. Surveys involved transects, dip-netting in waterbodies, and casual observations along trails and roads. Each individual observed was identified to the lowest possible taxonomic level, its position was recorded, and in case of capture it was released thereafter in the same place. All captures were conducted in accordance with the Portuguese laws and carried out under authorized licences 186/2009/CAPT (Instituto da Conservacão da Natureza e Florestas).