The changes in depth, temperature, water conductivity, and dissolved oxygen concentration in six floodplain lakes are described in regard to the dynamics of spring flooding and overgrowth by macrophytes. The influence of these factors on the composition and structure of macrozoobenthos communities is analyzed. The observed number of species refers to 60% of the theoretically predicted, which allows us to assume that the fauna has been identified sufficiently enough to analyze the interannual changes. Six families of invertebrates, which form together 55% of the fauna, are the richest in species number. The distribution of species by families also confirms enough data on the fauna representing in the obtained and analyzed samples. Abundance of only two species depend significantly on environmental characteristics; the taxonomic and trophic groups exhibit more links to the environment. Totally, 45 mutually associated species (43.7% of the total list) have been identified; they form 8 groups that are characterized by connectivity of the species composition ranging as 0.28–1.0 link/species, the average connectivity strength of 0.67–0.80, and the strength of species connectivity of 0.38–0.84 (the last index is proposed for the first time). Groups of mutually associated species may be defined as “faunistic cores of communities” confined to certain lakes and/or years of study. According to the redundancy analysis with multidimensional scaling ordination, the environmental factors affect the quantitative characteristics and overall taxonomic richness of communities. The indices, describing the structure of communities, do not depend on the analyzed factors, which is also confirmed by correlation analysis.