Purpose: To analyze, identify, and account for all costs associated with unproductive downtime of wagons during the interaction between rail and sea transport. At the seaport - railway station level, the technology of cargo transfer is particularly relevant. The choice of the technological option for cargo transfer in the context of limited resources for railway infrastructure and traction rolling stock must be economically justified. The direct transfer of cargo from one mode of transport to the other has been shown to increase the risks of unproductive downtime of wagons. This is due to the technologically and organizationally challenging nature of simultaneously preparing a vessel and supplying wagons for cargo operations. It is recommended that all costs associated with potential unproductive downtime of wagons be identified and taken into account. Methods: Analysis, synthesis, and formalization of aforementioned concepts is of paramount importance. Results: It has been determined that the base rates stipulated in the “Tariff Guide No. 2” do not encompass all the expenses associated with unproductive idle time of wagons. A range of values for the cost of unproductive downtime was collated for JSC “Russian Railways” and the operator companies for two scenarios of shunting services. This was undertaken with consideration for the varying cost per locomotive-hour of shunting work. Diagrams of data detailing the costs of unproductive idle time of wagons by various categories have been constructed. The technological solution of cargo overloading in the interaction of railway and sea transport using the terminal has been substantiated. Practical significance: The findings of the study can be of significance for the organization of operations at portside stations and railway areas for JSC “Russian Railways” and operator companies. Hidden costs of wagon unproductive idle time for both variants of shunting services have been identified for JSC Russian Railways and the operator companies.