Complex interactions between zooplankton and microbial food webs are vital to the ecosystem ecology of shallow lakes. However, little is known about how horizontal changes in environmental conditions may influence microbial and metazoan communities in shallow lakes. The specific goals of the study were i) to describe environmental variables responsible for the distribution of bacteria, flagellates, ciliates and crustaceans in an adjacent canal, ecotone and reservoir (littoral-pelagic zone) in two different types of lakes (Ceratophyllum-dominated and Potamogeton-dominated lakes); ii) to determine whether the contact zone waters differ in hydrochemical and biological terms from the waters of the canal and the open water zone; iii) and to evaluate the influence of particular macro-habitats (canal, canal/reservoir, littoral and pelagic zone) on the interactions between components of the planktonic food web. We studied four shallow, eutrophic lakes in Polesie Lubelskie (eastern Poland). The highest diversity and abundance of microorganisms and crustaceans were observed in the canal-reservoir contact zone, while the lowest values were noted in the pelagic zone. Hence, the contact zone in the investigated lakes could fulfil the function of an ecotone, distinguished by a significant increase in biodiversity, abundance, and species specificity of micro- and macroorganisms. Weak relations between food web components were found in the Ceratophyllum-dominated lakes, where environmental variables explained the bulk of the total variance in plankton abundance, whereas in the Potamogeton-dominated lakes, where environmental variables had a minor role in the total variance in plankton abundance, strong predator-prey relations were noted. Spatial structure of habitats proved to be another important factor for relationships between food web components, as our study indicated that habitat complexity can reduce negative correlations between food web components. 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.