The entire estuary water is dominated by the discharge of the River Odra into the Szczecin Lagoon. The water body is brackish and the salinity in the central part ranges 0.5 and 2 PSU. The Lagoon has a long eutrophication history; usually, two phytoplankton biomass peaks are observed: Diatoms in spring and blue-green algae in summer. The recent data on zooplankton is limited. Rotifers and Cladocerans supply the bulk of the zooplankton biomass. The ichtiofauna is composed of fresh and brackish water, migratory and marine species. Zooplankton and water samples were collected during 2003–2005. The results suggest that during 10 season’s climate in Odra River estuary, Cladocera were the dominant group, large impact on the density of mesozooplankton were: Daphnia cucullata and Daphnia longispina, Copepoda played a lesser role in the Odra River estuary than Cladocera. Biomass of mesozooplankton from the Lagoon was significantly higher compared with the biomass of mesozooplankton from Odra River estuary, which could be related to a greater inflow of nutrients into the Lagoon and the increased growth of phytoplankton, which forms an excellent first stage food web for herbivorous and carnivorous zooplankton, and fish and consequently cormorants.