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    The dataset contains abundance and biomass for different taxonomical units of phytoplankton (from phylum to species, according to identification accuracy) sampled from Estonian open and coastal waters in the Baltic Sea. Samples are collected with Ferrybox method (sampling depth appr. 5m) or by pooling samples from discrete depths (1, 5 and 10m) in national monitoring stations. Phytoplankton identification and enumeration was carried out using microscopy, biomass calculations were done using volume formulas provided by HELCOM-PEG (phytoplankton expert group) and published in (PEG BIOVOLUME).