Complex interactions between epiphytic fauna and microbial food webs in periphyton are vital to the ecosystem ecology of shallow lakes. However, little is known about how different types of macrophyte dominated lakes may influence microbial and metazoan communities. The goal of the present study was to examine the impact of metazoan on microbial food web in three different types of lakes (Stratiotes-dominated, Ceratophyllum-dominated and Potamogeton-dominated). The results of this study suggest a strong correlations between chironomid larvae, small Metazoa and microbial communities in the periphyton of macrophyte-dominated lakes. Weak relations between food web components were found in the Potamogeton-dominated and Ceratophyllum-dominated lakes, where environmental variables explained the bulk of the total variance in periphyton abundance, whereas strong predator-prey relations were noted in the Stratiotes-dominated lake, where environmental variables had a minor role in the total variance in periphyton abundance. Our study contributes to knowledge of the functioning of eutrophic lakes in the current era of increasing eutrophication caused by climate change and human activity.