The pelagic primary production in the Baltic Sea ranges from 100 to 175 mg C m−2 y−1, depending on the sub-basin. Phytoplankton productivity, total biomass, and species composition show strong seasonality. Around half of the annual carbon fixation takes place during the spring bloom. The proportion of diatoms to dinoflagellates in the phytoplankton has distinct seasonal and spatial patterns as well as decadal-scale trends and has been ascribed to climate-related factors, particularly the harshness of winter. The diatom/dinoflagellate ratio reflects the change in the dominant energy transfer pathway into the pelagic or benthic foodwebs as sedimentation of diatoms is much faster than that of dinoflagellates.
The spring bloom is terminated by nitrogen limitation in most of the Baltic Sea; consequently, the pelagic community switches to a functionally more diverse community around May–June. A shift towards earlier, more prolonged spring blooms (but with lower average biomass) has taken place in the central Baltic Sea over the past 20 years. Chlorophyll concentrations have remained essentially unchanged during the past few decades (1990–2016), with the exception of the westernmost parts of the Baltic Sea, where it shows decreasing trends. On a decadal scale, the Baltic Sea summer phytoplankton community composition has gone through a gradual shift, most notably an increase in species richness, with subsequent effects on ecosystem functions. Some of this increase in species richness may be due to anthropogenic vectors.
Phytoplankton blooms are a natural phenomenon in the Baltic Sea ecosystem, with blooms in late summer dominated by nitrogen-fixing cyanobacteria. However, due to eutrophication the phytoplankton blooms become more frequent and extensive. In the coastal areas of the northern Baltic Sea, the symptoms of eutrophication are seen as e.g. decreased water clarity and an increased amount of filamentous algae.