The dataset contains records of bats (Chiroptera) collected in the lower valley of River Sabor (NE Portugal), in the scope of the long-term Ecological Monitoring Program (PME) of the Baixo Sabor Hydroelectric Dams (AHBS), promoted by EDP – Energias de Portugal, S.A. Specifically, this dataset includes results of surveys made in the scope of the monitoring of the project of Compensation Habitat of Vilariça valley for Chiroptera (MC1). Data were collected between April 2013 and August 2014, during field visits to 2 selected points located along the Vilariça stream, a tributary of the Sabor river, located near its mouth. The presence and identity of bat species were assessed by acoustic sampling of the echo-location calls emitted in fligth. The records include taxa identified at the species, genus, family or order level, as well as groups of species that share common calls but cannot be identified to any taxonomic level, and that were thus assigned to acoustic “species complexes”.