The biomass and composition of the phytoplankton was studied at seven sampling stations located at different water bodies (open water, inner pond and canal) of a large, shallow turbid lake (Lake Fertő, Neusiedlersee). The open water was characterized by picocyanobacteria and meroplanktonic diatoms, the artificial canal by epiphytic diatoms, cryptophytes and chlorophytes. The inner ponds, based on the phytoplankton composition, were positioned between these water bodies. High picoplankton abundance (>106 cells.mL−1) and predominance (up to 80% contribution to the total phytoplankton biomass) were detected in the open water and the inner ponds, which was hypothesized to be the result of the turbid environment by the suppression of the top down control and by light-limitation. Information on the diversity of the picoplankton in the open water of the lake has been presented first time in this study. Based on molecular analysis (16S rRNA gene and cpcBA-IGS region) the dominant group of picocyanobacteria belonged to the Cyanobium gracile cluster (group A) of the picophytoplankton clade in April. Members of two other picocyanobacterial groups (group B and C) were also detected.