The dissertation reveals the consequences of the influence of hydromorphological changes of aquatic ecosystems of the Azov-Black Sea region on the processes of biological invasions of alien species of macroinvertebrates. The multifaceted impact of new approaches to ballast water management on the risks of bioinvasions at the global level of the process and at the level of the individual marine ecosystem has been revealed. The tendency of expansion of exotic species of marine origin in large river systems, which are under the simultaneous influence of climate change and regulation of runoff, has been revealed. The methodological problem of cryptic invasions in the ecosystems of temporary ponds is revealed. Reconstruction and reclassification of historical groups of relict Ponto-Caspian fauna in the context of the theory of functional trophic groups is carried out. The status of Ponto-Caspian relict fauna species has been categorized according to IUCN methods. For the first time for the Azov-Black Sea region, the connection of biopollution with hydromorphological conditions of the shores was revealed, the mechanisms of influence of separate components of hydromorphological degradation on the supralittoral fauna and biopollution processes in the surf zone were described. For estuaries of the Azov-Black Sea basin, specific processes of biological pollution during the transformation of the salinity regime of estuaries and artificial fragmentation of estuaries have been revealed. The ecotone ecosystem "small stream - sea", its communities and specific processes of biological pollution are described. For large river basins, a variety of scenarios for the expansion of the Ponto-Caspian fauna are described. For the first time, the phenomenon of expansion of the endemic fauna of the Caspian Sea into the Azov Sea basin is comprehensively described. Using the EUNIS classification of habitats, the distribution of alien species in different types of habitats is described and analyzed. The functional connection of groups and habitats in the processes of biopollution in the context of the theory of functional feeding groups is revealed. A number of new communities with dominance of exotic species formed in aquatic ecosystems of the Azov-Black Sea basin are described. A variety of scenarios of the links between biopollution and water quality, which are formed in different types of aquatic ecosystems and are related to the diversity of ecological preferences of native and invasive species, have been identified. The dissertation largely provides a basis for further development of monitoring systems, environmental assessments and environmental management in the Azov-Black Sea region, in particular in the context of integration of Ukrainian legislation with a number of European and international directives and conventions: Water Framework Directive, Marine Strategy Framework Directive, Bern etc. Approaches to the marine coastal bioindication with the use of habitats, supralittoral species, and communities for the needs of ecological assessments according to the requirements of European directives have been developed. At the same time, a zoning scheme of the Black Sea coasts according to hydromorphological criteria was developed, a regional list of marine habitats with the allocation of new and uncodified habitats was identified, and the stability of indicators to the "estuarine quality" paradox was tested. The results of the research were used in a number of working groups of Ukrainian governmental, regional and departmental structures, official discussion of legislative documents, preparation of working documents and reports for the Berne Convention, the Convention on Biological Diversity, the Black Sea Commission and others. In the field of nature conservation, research results were used to create international IUCN Red Lists, regional lists of rare species, development of the State Cadastre of Fauna of Ukraine, substantiation of Emerald network areas, nature chronicles of many conservation institutions and proposals for a new edition of Red Book of Ukraine. The results of research were used in the field of science popularization and extracurricular education (educational and scientific programs in a large number of youth expeditions, schools and trainings, schools of environmental journalism, other activities; preparation of student research papers; popular science lectures).