The dataset contains records of Phytobenthos (Diatoms) collected in the watershed of River Sabor, and included in the Ecological Monitoring Program (2015-2019) of the Environmental Impact Assessment of the Foz Tua Hydroelectric Dam, promoted by EDP – Energias de Portugal, S.A. Data were collected in the springs of 2015-2019 during field visits to three sampling points located upstream the reservoir, including the intersection with river Maçãs, 7 kms upstream. The present Ecological Monitoring Program (2015-2019) aims to evaluate the impacts of the onset of exploration phase in the water quality of the river. The occurrence of the target taxa was documented through 8449 records of species presence and number of individuals (valve counts).