Anthropogenic and natural climate-impacted water level (WL) fluctuations are one of many environmental problems affecting natural ecosystems. The aim of this study was to explain differences in the development of autotrophic and heterotrophic plankton in two shallow, temperate, embanked lakes with different modes of WL regulation. Lake Mytycze has natural WL changes supplied exclusively by precipitation; a decrease in water level was predominantly due to more evaporation than precipitation. In this lake, nutrient concentration, particulate matter, growth of toxigenic cyanobacteria and contamination with microcystins correlated positively with decreases in WL. Lake Tomaszne has anthropogenic WL regulation, elevated values of nutrients and particulate matter, but they were caused by the periodic, abrupt entrance of river waters rich in allochthonous nutrients, organic and inorganic particles. In this lake, a higher biomass of cyanobacteria was observed than in the lake with natural WL changes; the concentrations of intracellular microcystins in water correlated positively with the biomass of toxigenic species. In both lakes, decreases in the biomass of algivorous crustaceans correlated with the occurrence of cyanobacterial biomass. Biomasses of algivorous crustaceans increased abruptly when concentration of microcystins diminished below 2 μg∙dm−3. These biomass peaks occurred due to rapid development of the cladocerans; Bosmina longirostris was found in the lake with natural WL changes and Daphnia cucullata was found in the lake with anthropogenic WL regulation. The development of predacious crustaceans was not related to the blooms of filamentous cyanobacteria or the biomass of algivorous crustaceans (as potential prey). In both lakes, Thermocyclops crassus and Mesocyclops leuckartii (Copepoda) contributed significantly to the biomass of predacious crustaceans; their abundance correlated positively with the amount of particulate matter, which was probably utilised as an alternative food source. These findings illustrate indirect influence of WL on plankton composition and biomass through alteration of environmental variables. The results indicate that the mode of WL regulation (natural vs anthropogenic) must be taken into consideration when estimating the influence of WL changes on plankton dynamics.