The study investigated the effect of microhabitat (emergent/submerged macrophytes) within lakes of different status (transparent/cloudy water) on the diversity and distribution of chironomid assemblages. Field and laboratory studies were undertaken bimonthly, from January to November 2008, in two shallow lakes of Polesie Lubelskie (eastern Poland), transparent water and cloudy water lake. The main objectives of the study were to compare the density and taxonomic richness of chironomids associated with emergent and submerged macrophytes within lakes of extremely different environmental conditions and to recognize the most important variables affected chironomid distribution between microhabitats within lakes. In transparent water lake, number of chironomid taxa varied between 12 (emergent macrophytes) and 18 taxa (submerged macrophytes) and was significantly higher than in cloudy water lake, 6 and 8 taxa, respectively. Mean abundance of chironomids associated with emergent macrophytes was higher in cloudy water lake. The opposite relation was observed on submerged macrophytes. The PCA analysis showed visible distinction of chironomid assemblages between microhabitats and lake types. The results of RDA led to determine the significant variables (Monte-Carlo permutation test) affected chironomid distribution. In both, transparent and cloudy water lake, the significant variables responsible for chironomids distinction between microhabitats were density and biomass of macrophytes, biomass of periphytic algae and pH. Moreover, nutrients, N-NO₃ (transparent water lake) and P-PO₄ (cloudy water lake), showed the significant influence.