The present work is aimed at solving urgent problems related to ensuring environmental safety of port activities, economic development of sea transport and environmental protection in the Baltic Sea region. On this basis priorities of environmental policy in the port sector shall be defined, system of environmental planning and monitoring shall be established and methods of port environmental management shall be developed. Proceeding from the topicality of the problem the present work boils down to practical implementation of sustainable development principles to integrated management of economic and ecological activities in port complexes through environmental management system as the most important component of economic development. The subject of the research is environmental management system (EMS) in seaports of the Baltic region and its functional elements. The aim of the work is to define the economic and geographical peculiarities of the ecological management system formation in the port complexes of the Baltic region and to develop the ecological status indicators (ESI) as the main tool of the EMS.