In spite of the existence of a number of papers applying the biomarker approach using pigments or akinetes to discuss the impact of cyanobacteria on the functioning of lakes in the palaeoenvironmental context, their sedimentary imprint in the form of microcystins (MCs) has never been taken into consideration. Our objective was to reconstruct 200 years of the development of chironomid assemblages in a shallow Polish lake with notoriously blooming toxic cyanobacteria. A 50-cm long sediment core sampled from the central part of the lake was sliced every 1 cm, dated, and analysed for the subfossil remains of Chironomidae and concentrations of MCs. The fauna underwent four distinct stages in its recent history: three periods when the assemblages were typical of hypertrophic conditions (the first one comprising the entire nineteenth century, and the second and third one including approximately the last 30 years of the twentieth century), separated by a ''eutrophic'' assemblage during the first 70 years of the twentieth century. The typical features of the ''eutrophic'' midge assemblage were high total densities and high values of taxonomic richness and diversity. This period coincided with relatively low concentrations of MCs in the sediments. Sediments from the hypertrophic periods were distinguished by taxonomic impoverishment of chironomids, low Shannon diversity index, a strong decrease in chironomid numbers, and high concentrations of MCs. Significant negative correlations with MCs along the sediment profile were observed for eurytopic chironomids. MC concentrations were also negatively but not significantly correlated with total density of chironomids, their benthic and epiphytic assemblages, species richness, and diversity index.