The dataset contains Phytoplankton records of samples collected at Baixo Sabor reservoir during the first year of the Ecology Monitoring Program (PME) of Baixo Sabor Hydroelectric Scheme, promoted by EDP – Energias de Portugal, S.A. Samples were collected in the deeper zone of the reservoir, at a fixed station 1300 m upstream of the dam, in 6 campaigns carried out between March and October of 2016. The targeted taxa were phytoplankton species, included as biological quality element for ecological quality in the framework of the EU’s Water Directive.