Structural and functional parameters of planktonic and benthic communities in the White Sea were studied both at the sites of industrial mussel cultivation farms (MF) and in aquaculture free areas. Redistribution of organic matter in pelagic and bottom systems close to MF was shown to result in changes of the structure of the surrounding biocoenoses. The consumption of proteins by mussels led to a drastic decrease in the relative abundance of planktonic bacteria, while the composition and abundance of the zooplanktonic community were not affected by MF. A significantly uneven distribution was found in the bottom habitats, which results in organic contamination and, in some cases, in degradation of benthic communities.