Species composition and quantitative structure of small-sized Cladocera community and their algal diet before, during and after cyanobacterial blooms were studied in highly eutrophic lake. The objective of the study was to investigate, how the mass development of toxin-producing cyanobacteria affect the abundances of small-sized Cladocera and their preferences within consumed algal cells. Cyanobacterial blooms were predominantly constituted by microcystin-producing genera Planktothrix, Dolichospermum, Microcystis. The concentration of intracellular microcystins in lake water ranged 0.0–23.61 μg dm−3. Bosmina longirostris, B. coregonii, Diaphanosoma brachyurum and Daphnia cucullata were dominant in Cladocera community. The highest abundances of B. longirostris occurred in periods without cyanobacterial blooms and B. coregonii during blooms and after them. The maximum abundances of D. cucullata were observed before and after the cyanobacterial blooms, while the abundance of D. brachyurum was the highest at the beginning of blooms. Small Bacillariophyceae, small Chlorophyceae and Cryptophyceae were the most abundant among identified algal cells detected in digestive tracts of the Cladocera dominants. Tracts of D. cucullata, B. longirostris and B. coregonii contained the highest number of Bacillariophyceae always before blooms. During cyanobacterial blooms, cells of small Chlorophyceae predominated in tracts of D. cucullata. After bloom, cells of Cryptomonas spp. were mainly consumed both by D. cucullata and by B. coregonii. Fragments of Dolichospermum spp., besides Bacillariophyceae and Cryptomonas spp. cells, were occasionally found in tracts of D. brachyurum. Our study indicated that blooms constituted by toxin-producing cyanobacteria may influence quantitative and qualitative structure of the small-sized Cladocera community.