The current geological exploration works in the internal sea waters, territorial sea and on the continental shelf of Russia by investors of various forms of ownership are not provided to the necessary extent by the regulatory and legal framework that allows to establish the amount of payments for the right of prospecting, evaluation and exploration of mineral deposits. The essence of the proposed methodology for calculating the payment for subsoil use on the shelf is to assess the ranking potential of a particular object according to a group of rank-forming factors: general, geological, physical-geographical, economic-geographical, environmental. All developments are based on the level of profitability, which determines the efficiency of any project realization. Justification and consideration of the above conditions when determining the rates of payments for subsoil use will be realized in the information-analytical system (IAS) "Register of shelf zones of the Russian Federation". The Register will meet the current level of geological knowledge, allow mobile and flexible input of new clarifying data, carry out necessary calculations and analytical actions. The registry will be closed from unauthorized access and simple enough for a potential user.