-The role of environmental factors in aquatic ecosystems results from basic lake characteristics, human disturbances ('cultural eutrophication') and climate-related trends in the physical and chemical components of lakes. Although the influence of environmental factors on the abundance of aquatic animals is fairly well documented, less has been done to research their influence on food web interactions. The aim of the study was to evaluate microbial and classical food webs in lakes, with special emphasis placed on the role of environmental factors as influencing strengths. Variation partitioning, based on redundancy analysis, revealed that environmental factors played the most important role in structuring aquatic communities by accounting for 87.5% of their variation. Among all the factors measured, total solids (TS), transparency (Secchi disc) and temperature were most closely related to the variation in trophic communities. The analyses of food web interactions under low and high levels of those factors revealed that they differently influenced strengths among food web components. The strongest relations among distinct trophic levels were found under conditions of low TS, the lowest number of relations was found under conditions of low temperature. Only in low TS did bacteria correlate significantly with biogenes. Under high TS, bacteria positively influenced plenty of higher trophic levels. Top-down control was observed under conditions of high temperature. Conditions of low and high transparency did not diversify food web interactions. The obtained results can broaden our knowledge of the response of food webs to environmental factors in advanced stages of global eutrophication of water bodies and in the early stage of projected trends of global climate change.