The changes in phytoplankton pigment compositions and concentrations during a 20-year period of exploration of the Baltic Sea have been analysed. Both chlorophylls and carotenoids are characterized in the context of their monthly variations in the Gulf of Gdańsk and the open waters of southern Baltic Sea. It is assumed that pigment compositions are good markers of environmental changes, especially in the context of phytoplankton composition and biomass growth. Long-term trends and changes for both regions are established on the basis of marker pigment analyses for a period of two decades (1999–2018). Chlorophyll a, a marker of phytoplankton biomass, is clearly decreasing in both regions: −2.11% yr−1 (slope of trend curve −0.21) in the Gulf of Gdańsk and −2.41% yr−1 (slope −0.08) in the southern Baltic. Decreasing trends for several marker pigments have also been noted in both regions for the period in question, namely, fucoxanthin (diatom marker): −0.10% yr−1 in the Gulf of Gdańsk and the southern Baltic (respective slopes −0.0012 and −0.0003); alloxanthin (cryptophyte marker): −2.28% yr−1 (slope −0.012) in the Gulf of Gdańsk and −0.54% yr−1 (slope −0.001) in the southern Baltic; peridinin (dinoflagellate marker): −4.35% yr−1 (slope −0.05) in the Gulf of Gdańsk and −5.55% yr−1 (slope −0.02) in the southern Baltic. The decreases in the average concentrations of chlorophyll b (−1.30% yr−1, slope −0.008) and neoxanthin (−1.37% yr−1, slope −0.0014) have been slower in the Gulf of Gdańsk than in the southern Baltic (−3.31% yr−1, slope −0.013, and −3.38% yr−1, slope −0.0019 – respectively). In contrast, the yearly mean concentrations of zeaxanthin (the main cyanobacteria carotenoid) have increased significantly, to 7.16% yr−1 (slope 0.016) in the Gulf of Gdańsk and 1.45% yr−1 (slope 0.0022) in the southern Baltic. This may be the consequence of the reduced riverine supply of nutrients to these regions in recent years. The results indicate that the ecosystem of the Gulf of Gdańsk is responding more dynamically to eutrophication-related changes than the open waters of the southern Baltic Sea.