This work studies the composition and abundances of phytoplankton and zooplankton and their relationships during cyanobacteria bloom (mainly Dolichospermum lemmermannii) in two subarctic oligotrophic lakes, a clear deep lake (Krivoe) and a brown shallow lake (Krugloe). Cyanobacteria bloom (D. lemmermannii) was observed four times during 7–10 days in both lakes: late July, late August, September 2019, and late September 2020. The toxicity of cyanobacteria was determined by the presence of cyanotoxins in water and plankton biomass. Microcystins (mostly LR, RR, and other structure variants) were found in every case of visible blooms (July–September of 2019–2020) in the shallow lake and only once in the deep lake. Despite the nutritious food items (cryptomonads), the presence and dominance of colony-forming microalgae (Botryococcus brauni) and filamentous cyanobacteria in both lakes consisted of a low-efficient food base for grazers. A high abundance of toxic microcystins in the shallow lake with dystrophic features led to the specific composition of zooplankton with the prevalence of the selective grazers, copepod Eudiaptomus graciloides, and cladoceran Ceriodaphnia pulchella adapted to cyanotoxins. In a clear deep lake, where toxic variants of microcystins were low or not detected during the cyanobacteria bloom, the omnivorous rotifer Asplanchna priodonta and small grazer Bosmina longirostris reached high abundance. This study confirms close relationships between cyanobacteria and zooplankton communities.