The dataset contains records of Herpetofauna (Amphibia and occasional Reptilia) collected in the lower valley of the River Sabor (NE Portugal), in the scope of the compensatory measure MC10 (sub-measures MC10.1, MC10.2, MC10.4 and MC10.5) and MC2 (sub-measure MC2.4) included in the long-term Compensatory Measures Monitoring Program (PMC) of the Baixo Sabor Hydroelectric Dams (AHBS), promoted by EDP – Energias de Portugal, S.A. This dataset includes results of surveys carried out in and around the area affected by the dam, from March 2015 to October 2020. Although the target group were the Amphibian, several observations of reptiles recorded in the framework of MC10.4 were also included. Sampling was performed by visual surveys in line transects (MC10.1), stationary points (MC10.2), and intensive search/dip netting (MC10.4, MC10.5 and MC2.4) along the lower Sabor river valley (including some tributaries) and in the rivers Maçãs and Angueira, up to 42 km upstream. The identification of the species was made "in situ". The dataset consists of 12833 individual observations (adults and larvae) of Amphibia and Reptilia, of which 12774 were identified to the species level, 25 to the genus and 34 to supra-specific levels (class to family).