At the present stage one of the most important factors in the economic growth of Russian regions is the production processes modernization based on the best available technologies (hereinafter—BAT), ensuring the reduction of the negative impact on the environment in cost-effective ways. The most important conditions for the successful implementation of BAT at regional enterprises is the creation of general institutional conditions at the all-Russian level and the supply of enterprises with domestic technologies meeting the criteria of the best available technology. Over the past several years, large-scale work has been carried out in Russia to amend legislation, prepare BAT reference documents, and form the institutional conditions for their implementation. However, sustainable outcomes in specific regions will require the further development of regional innovation systems, consistent with the needs of local enterprises in BAT. The article proposes a general regional mechanism for managing the sustainable development of an innovation system based on BAT. For its successful implementation, a set of practical recommendations for the Rostov region has been formed. Within the framework of the innovation regional infrastructure it was proposed to create a new institute for the implementation of BAT—the Regional BAT competence center, priority areas for the development of potential and promising BAT in the region were identified, a general pattern of interaction of the Regional BAT competence center with other participants in the process was developed.