There are presented the research results on the systemic automation of geoinformation support for security of autonomous navigation in the Arctic, under climate change. In the course of the research, there were used the methodological foundations of risk management technologies while developing natural – industrial systems. A structural model is proposed that combines investment goals with the costs of geoinformation security support in projects for the development of autonomous navigation in the Arctic. Based on the proposed model, a modular web-based tool has been given that implements systemic automation of geoinformation security for autonomous navigation in the Arctic under climate change. Examples of using the developed tool are given.