Predictably, epibenthic Cyclopoida, as part of the meiofauna, have an important role in the secondary production of the zoobenthos. However, studies on the diversity and abundance of epibenthic cyclopoids are still rare. As a result, knowledge regarding distribution of this group under varied environmental conditions is only sketchy. Here we present a comparative study of the community structure of epibenthic Cyclopoida in eutrophic lakes in relation to the physical and chemical characteristics of water and sediments, feeding conditions and grazing pressure from omnivorous fish. Low species diversity coincided with highly variable species composition of epibenthic cyclopoids; 2–9 species occurred in the lakes, but we found a unique species composition of the epibenthic community in each lake. Cyclopoid density ranged from 386 ind/m2 to 28 526 ind/m2. Canonical correspondence analysis indicated temperature, bacterioplankton biomass, concentration of total solids and content of organic matter in sediments as variables impacting the density of this group. As these variables are directly and indirectly connected to food recruitment, the results suggest that the taxonomic composition and abundance of epibenthic cyclopoids are regulated primarily by trophodynamics conditions.