The effects of climate-induced, long-term changes on mesozooplankton biomasses were studied based on monitoring data collected since 1966 in the northern Baltic Sea. We found that the biomasses of marine and brackish mesozooplankton had decreased significantly from 1966 to 2019, and a remarkable biomass and functional biodiversity loss took place in the mesozooplankton community. Our results put emphasis on the impact of two climate-driven regime shifts for the region's mesozooplankton community. The regime shifts took place in 1975 and 1976 and in 1989 and 1990, and they were the most important factor behind the abrupt biomass changes for marine mesozooplankton and total and marine Copepoda. Only the latter regime shift influenced the biomasses of brackish Copepoda, marine Cladocera, and total Rotifera. The decreasing length of the ice-cover period drove the decrease of the biomass of limnic Limnocalanus macrurus (Copepoda), while the winter North Atlantic Oscillation was behind biomass changes in the total and the brackish Cladocera. These findings may have important implications for planktivorous fish, such as Baltic herring, particularly in terms of their impact on commercial fishing.