The dataset contains records of the Otter (Lutra lutra) collected in the lower valley of the River Sabor (NE Portugal), in the scope of the long-term Ecological Monitoring Program (EMP) and the Compensatory Measures Monitoring Program (CMMP) 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 April 2015 to July 2020. Sampling was performed in transects distributed along the lower Sabor river valley (including some tributaries), and along the rivers Maçãs and Angueira, up to 73 km upstream. The presence and identity of the target species were assessed through the presence of faeces (spraints) and/or footprints of the target species.