Shallow lakes according to the alternative states theory may present extremely different environmental conditions, clear water with abundant growth of macrophytes and turbid water with cyanobacterial blooms. The deterioration of water quality led to visible changes within submerged macrophytes and thus in available habitats for plant-associated biocenosis. Larvae of chironomids are the most numerous and widely distributed macroinvertebrates. Since benthic chironomids are used in the monitoring of environmental changes and in paleolimnological research, epiphytic chironomids are not well known in this regard. The larvae can be used as indicators of lake macrophyte status. The present study focuses on plant-associated chironomids of a group of ten shallow lakes of the Polesie region (eastern Poland). The lakes were classified with alternative states theory as macrophyte-dominated (MD), phytoplankton–macrophyte-dominated (PMD) and phytoplankton-dominated (PD). The domination structure of epiphytic chironomids showed significant changes between lake types, with the highest abundance of Paratanytarsus austriacus in MD lakes, Endochironomus albipennis in PMD lakes and Cricotopus sp. (gr. sylvestris) in PD lakes. The highest mean density was noted in PD lakes while the highest species diversity (values of Shannon–Wiener index) in PMD lakes. Moreover, environmental variables (macrophyte biomass, Secchi disc depth, chlorophyll-a and TP) differentiating lake types were used in RDA analysis to evaluate their effect on chironomid taxa distribution. Next, the variables with a significant effect on specific chironomid taxa were used in multivariate regression analysis. The results led to the creation of a model of distribution of chironomid taxa with regard to lake type.