The dataset contains records of cliff-nesting species of high conservation priority, namely birds of prey (Aves, Accipitriformes and Falconiformes) and Black Stork (Ciconia ciconia) (Aves, Ciconiiformes) collected in the lower 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. The dataset includes results of surveys made in and around the area affected by the dam, from February 2010 to September 2014. Data consists of observations of the target species performed in fixed sampling points directed to birds of prey. Observations were made around the Sabor river, from its mouth to 42 km upstream. The presence and identity of bird species were assessed by visual and/or acoustic observation with binoculars and/or telescope. The records include taxa identified at the species level.