The thickness and duration of ice cover are strongly influenced by global warming. The aim of this study was to determine chemical (organic carbon, total nitrogen and phosphorus concentrations) and biological (nanoflagellates, ciliates, phytoplankton, rotifers, crustaceans) parameters under the ice cover in three eutrophic lakes (Masurian Lake District, Poland), differing in their morphometry and fisheries management. All the studied groups of organisms showed high variability over a short time. Taxonomic composition of planktonic communities, except for rotifers and phytoplankton, was similar in all lakes. Nanoflagellates were dominated by autotrophic forms, while ciliates were primarily composed of small oligotrichs and prostomatids. Nano-sized diatoms and mixotrophic cryptophytes were the most important components of phytoplankton and they formed an under-ice bloom in one lake only. Rotifers were mainly represented by Keratella cochlearis, Polyarthra dolichoptera and Asplanchna priodonta. Among crustaceans, copepods clearly dominated over cladocerans. Our research suggests that winter was a very dynamic period. In the under-ice conditions, pelagic organisms were strongly dependent on each other. The shallow lake and the deeper, small lake differed significantly in nutrient and chlorophyll concentrations, ciliate and phytoplankton biomass and the ratio of autotrophic to heterotrophic biomass. These results suggest that morphometric parameters may affect planktonic organisms during the ice-covered period.