Basic principles of the multidisciplinary approach to arctic marine transport systems (MTS) design and analysis are described in the article. The main idea of the approach is to synthesize geographic information system (GIS) technologies, different shipbuilding disciplines, fleet planning instruments and agent-based dynamic simulation models in an integrated software framework on the basis of object-oriented programming Vessel operation is described as the movement and interaction of independent ships in GIS environment within the framework of the simulation model. MTS operation combines vessel operation itself (routing, determination of speed and fuel consumption, icebreaker escort, etc.) with plenty of external entities (port infrastructure, ice channel freezing process, offshore platform operation, etc.) that could be described as systems with comprehensive logic and physical behavior. Such integration provides a new quality of MTS simulation that allows considering complex interconnection of various subsystems and all the important details of each MTS project. The outline of the program framework to realize such an approach is given, and two case studies are described to demonstrate its capabilities and feasibility.