The research of epiphytic microfauna was conducted during the summer months (July, August, September) of 2012 in three localities (Zajarki Gravel-pit, Škrčev kut Oxbow and Sutla Backwater) with various intensity of anthropogenic impacts. The basic hypothesis of this study were: (i) the complexity of macrophytes habitus increases the diversity and abundance of epiphyton (ii) different methods of fixing the samples affect the results of the qualitative and quantitative composition of the epiphytic microfauna. Main goals of this study were to determine: 1) differences in the diversity and abundance of epiphytic microfauna due to habitat structure (complex and simple) of aquatic macrophytes; 2) differences in the diversity and abundance of epiphytic microfauna considering microhabitats (within macrophyte stands on the edge and in the macrophyte stands); 3) the impact of different methods of sample fixation on the results of epiphyton community structure. An analysis of physico-chemical parameters showed statistically significant spatial changes of water conductivity, total suspended solids, turbidity, nitrite, nitrate, total nitrogen, chemical oxygen demand, chlorophyll a from plancton and epiphyton and POM between three water bodies. Given the complexity of macrophytes habitus the higher abundance and diversity of epiphytic microfauna was recorded in water body with submerged macrophytes, where all studied groups of microfauna have achieved their highest abundance, and overall structure of the microfauna dominated by Ciliophora. The gravelpit with floatant macrophytes was observed with statistically the smallest abundance and diversity of taxa Testacea, Rotifera and Gastrotricha. In the oxbow with a high degree of trophy and small cover percentages of floatant macrophytes recorded a large number of individual groups of Testacea, Rotifera and Gastrotricha but with small diversity. Among the investigated microhabitats on the edge and inside the macrophytes stands was no statistically significant differences in the structure of the microfauna, although edge of macrophytes stands showed a higher diversity of species. Results of statistical analyzes indicate that the number of the epiphytic microfauna positively correlated with food sources in epiphytic algae, suspended and dissolved organic particles and phytoplankton. Comparing the structure of the microfauna in live and fixed material, a significant decrease of taxa Ciliophora showed while Rotifera showed significantly better for the determination and quantitative analysis in fixed material. Consequently, different ways of processing collected materials require each comparison in the interpretation so the results would be as complete as possible. Results of this study indicate that different forms of anthropogenic activities affect the environmental conditions of individual water body and changes in the structure of biocenoses.