Efficient transport solutions are based on multimodal systems, with the dominant role of rail and road transport in land versions of the systems and the connecting and directing part of intermodal terminals, transhipment terminals or warehouse centres. The implementation of transport processes is always associated with the risk of lack of timeliness (quality) or threats to people, equipment and cargo (safety) resulting from human, technical, organizational and global factors like pandemics or war. The article contains a risk mapping method in multimodal transport systems configured to estimate the risk of lowering the quality of logistics services (on-time deliveries, etc.). The method combines factors usually considered separately in studies on individual modes of transport. A formal notation of risk factors as a mathematical model was proposed, and a case study was provided to picture the implementation.