Monitoring data of phytoplankton abundance and biomass (1979-1999) and Chl. a (1979-2000) from surface samples (0-10 m) of the Kattegat, Belt Sea and Baltic proper were investigated for long-term trends. The Mann-Kendall test as well as the LOESS smoother was applied for three taxonomic groups in spring, summer and autumn separately. Chl. a trends were analysed by linear regression. Downward trends were found for diatoms in spring and summer whereas dinoflagellates generally increased in the Baltic proper but decreased in the Kattegat. In autumn, diatoms increased at some stations. For cyanobacteria, downward trends were detected mainly in the Kattegat/Belt Sea area. Chl. a concentrations showed a general decrease in the Kattegat/Belt Sea area but an increase in the Baltic proper. Observed changes in trends during the two decades might indicate shifts in the ecosystem.