The phytoplankton biomass data of the period 1979–2005 of the Belt Sea area and the Baltic Proper, separated into spring, summer and autumn data, were checked for trends, together with the relevant abiotic factors (temperature, salinity, and nutrient concentrations). The Mann–Kendall test was used for detecting monotonic trends over the whole investigation period or, if trend breaks occurred, over the period before and after the trend breaks. The relationships between phytoplankton community composition and the environmental variables were assessed by a redundancy analysis (RDA), which could support some results of the trend analyses. Water temperature increased but salinity and inorganic nitrogen concentrations decreased in the southern Baltic Proper. Spring phytoplankton biomass and chlorophyll a concentrations increased in the Baltic Proper and decreased in Mecklenburg Bight. The biomass of Diatomophyceae decreased in spring at some stations but increased in autumn. If the Diatomophyceae spring blooms decreased, the total Dinophyceae biomass increased. Strong spring blooms of Diatomophyceae occurred in the 1980s and since 2000, but those of Dinophyceae in the 1990s. These two groups showed alternating oscillations. Trends in most phytoplankton components were different in the Baltic Proper and the Belt Sea area, confirming that Darss Sill is a biological border.