The dataset contains records of Iberian Desman (Galemys pyrenaicus) collected in the river Sabor sub-basin (NE Portugal), in the scope of the long-term Ecological Monitoring Program (PME) [2012-2020] and the Compensatory Measures Monitoring Program (PMC) [2015-2020] of the Baixo Sabor Hydroelectric Dams (AHBS), promoted by EDP – Energias de Portugal, S.A. This dataset includes results of surveys carried out inside and around the area affected by the dam, from June 2012 to October 2020. Sampling was performed in transects distributed along the Sabor river valley and tributaries, in rivers Maçãs and Angueira and in Vilariça stream, up to 132 km upstream (132 km before 2015, and 120 km from 2015-2020) . The presence and identity of the target species were mostly assessed with scats attributable to them and validated, either by the traditional methods (presence of fur) [2012-2014], or by molecular means [>2015]. A total of 215 validated scats distributed by 60 occurrences was obtained, supplemented with an observation of one live individual.