Cyanobacterial blooms are regarded as a global environmental problem. The role of cyanobacteria in the food web of water bodies is still unclear. We have carried out an experimental study of invertebrate trophic relationships during the bloom of the cyanobacterium Aphanizomenon flos-aquae. The key links of the food web—plankton, microperiphyton, detritus, and benthic invertebrates—were collected for stable isotope analysis of carbon (δ13C) and nitrogen (δ15N) after 20-day exposure in mesocosms simulating the conditions of the near-shore biotope of the Rybinsk Reservoir without cyanobacteria (variant I) and with high abundance of cyanobacteria (variant II). Statistically significant differences in the δ15N values for crustaceans (Cladocera, Copepoda, Asellus aquaticus and Gmelinoides fasciatus), and mayfly larvae have been revealed between the variants: these values were 1–4‰ lower in the variant with cyanobacteria than in the variant without them. The cyanobacteria-induced shifts in the δ15N value for consumers indicate an assimilation of diazotrophic nitrogen and incorporation of cyanobacterial nutrients into their food chains.

The development of bacteria, phytoplankton, zooplankton, and microperiphytic organisms in artificial ecosystems, such as microcosms with aquatic plants, depressing algae (water soldier Stratiotes aloides L.), and plants not possessing a significant impact on them (arrowhead Sagittaria sagittifolia L.), was evaluated. It was shown that the zooplankton biomass did not decrease among water soldiers, despite the fact that the concentration of phytoplankton pigments was 2–3 times lower. The number of euplanktonic Cladocera has not declined, and the number of littoral and phytophilic Cladocera increased, but the number of Diaptomidae was lower. It is assumed that a large zooplankton biomass was produced by the use of bacteria and protozoa as an additional power supply to the algae. The share of zooplanktonic species consuming bacteria increased in microcosms with arrowhead. The number of predators increased and trophic relations between zooplankton and microperiphyton became closer in experimental systems with the plants of both species.

The distribution of zooplankton has been studied in a waterbody whose entire area is occupied by phytocenoses with the dominance of plants of different ecological groups. It is shown that, in the phytocoenosis of the submerged hydrophyte Elodea canadensis, zooplankton is involved in the classical grazing trophic web. The zooplankton community in this phytocoenosis is mainly made up by algaephagous species. In the habitats occupied by emergent plant Carex riparia, zooplankton is more closely associated with the components of the "microbial loop," where the most abundant groups are predators and bacterio-detritophagous species.

The influence of Stratiotes aloides L. (Hydrocharitaceae) on the formation of microperiphyton communities was investigated. In the presence of S. aloides (for more than 33 days), the total number of algal species and the numbers of blue-green algae decreased. The influence of S. aloides on individual species of Bacillariophyta and Chlorophyta is species-specific. It does not depend on the affiliation of algal species to certain ecological groups.

Changes in the structure of microperiphyton and zooplankton communities in the presence of hydrophytes Ceratophyllum demersum L. and Utricularia vulgaris L. have been studied. In experimental ecosystems with hydrophytes, the ratio of autotrophic to heterotrophic organisms and the abundance of Sarcomastigophora decreased while the number of infusorians in microperiphyton increased. The abundance of Rotifera and crustaceans of fam. Chydoridae increased significantly in zooplankton. Specific features of the structure of two communities depending on a plant species were noted. It was revealed that the species composition and abundance of microperiphyton and zooplankton in overgrowths of hydrophytes are closely related. Algae not consumed by zooplankters dominate in microperiphyton. The structure and ratio of heterotrophic organisms depended mainly on the abundance of zoophagous cyclops.