The dataset comprises phytoplankton observations from the Black Sea collected between 2006 and 2015 and processed by Boicenco L., Iordan M., Pantea E., Vlas O., and Voicu I. Sampling was conducted in Romanian coastal waters, ranging from shallow nearshore areas to the continental shelf, along several transects including Sulina, Mila 9, Portița, and Sfântu Gheorghe (northern region) as well as Constanța, Mangalia, and Vama Veche (southern region). Samples were obtained at standard depths using Niskin bottles, with 500 ml collected from each depth. Phytoplankton species were identified and counted from subsamples using an inverted microscope, and the total abundance and biomass of each species were calculated.