The Arctic zone of the Russian Federation is of strategic importance for the country. Considering the fragility of Arctic ecosystems, special attention needs to be paid to the sustainable development of transport and related infrastructure within the framework of the “blue economy” concept, which is relevant for Arctic waters. At the same time, it is necessary to identify the main factors and tasks of creating transport and port infrastructure, building a modern fleet, and organizing fisheries and tourism in an environmentally sound manner. The purpose of the study is to consider the problems of anthropogenic influence for seaport facilities and to create a conceptual model of an environmental risk management system. The existing problems of Arctic ports and infrastructure are analyzed and existing business processes are considered, taking into account the peculiarities of their functioning in Arctic conditions. To systematize environmental assessments and establish dependencies between the main indicators describing the impact of port activities on elements of the natural environment, ontological domain engineering is proposed. It systematizes the basic terminology used within different subject areas of ecology and risks and allows one to visualize the relationships between elements of the natural environment, objects, port systems, their parameters and impact factors to assess the impact of the seaport on the natural environment. The results of ontological engineering (design and development of ontologies) in the field of risk management are presented. Future research will be aimed at developing the applied aspect of applying the results of ontological engineering in terms of specific engineering studies related to the assessment of anthropogenic load on the Arctic territory using simulation modeling.