Abstract Studies on autotrophic picoplankton (APP; 3 μm) to low-temperature and low-light winter environment was confirmed by their higher maximum photosynthetic rate and light utilization parameter. Maximum photosynthetic rate and light saturation parameter increased significantly with both temperature and available light, but with different impact on the two size groups. Twenty-two picoeukaryotic strains were isolated and identified based on 18S rRNA gene sequence analysis. Taxonomic composition of the picoeukaryotic community in the studied shallow lakes was similar to other freshwater lakes in the temperate zone: members of genera Choricystis and Mychonastes were dominant, however, in Lake Balaton, common freshwater taxa such as Stichococcus bacillaris and Nannochloris bacillaris were also found.