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Estuarine fish communities are the common object of ecological studies that aim to infer the environmental changes occurring in estuarine environments and connected catchments. However, the high variability of abiotic factors inherent in estuarine water areas often makes the effects of eutrophication hardly distinguishable from those generated by other natural and/or anthropogenic fluctuations of hydrological and hydrochemical parameters. In addition, estuarine environmental zones of primary marine, fresh water, and brackish water characteristics can support diverse species communities with different sensitivity to various environmental factors. In the present work we clarified the structure of fish fauna in the lower Dniester and Dniester estuary area (northwestern Black Sea coast) and assessed its changes as a response to various environmental factors. We applied hierarchical clustering with successive indicator species analysis, and Random Forest analysis on the data on fish community parameters (species richness, diversity, and evenness) to discover that the area under study contains three separate fish communities, each with a different response to fluctuations of environmental factors. Subsequent examination of parasitological data readily confirmed the conclusion about presence of three fish communities. There is no simple universal indicator, such as abundance of a single species in any of the three communities, which can be used to monitor the eutrophication impact in the area of research. Instead, further analyses revealed the species diversity as a perspective indicator of eutrophication with nitrates in this water area.