The port areas are specific in terms of navigational accidents. Usually, accidents with low consequences dominate, but due to many users with contradictory needs, there is a requirement to keep the balance between business and safety. This balance is usually achieved by the Port Authority or like in Poland by Maritime Office together with Port Authority. Maritime Offices are the governmental body responsible to maintain the acceptable navigational safety level. Such an approach leads to several frictions between the users that needs are often contradictory. To ensure minimal safety level and introduce new or amended port regulations the scientific methods are demanded to support this process. The paper present methodology to adjust the port regulations of Kołobrzeg Port where the passenger ship owners moored in close vicinity of the waterway and therefore restricted it to the other users. The compromise was achieved with the application of real-time simulation method. Moreover, the paper presents the important role of harbor regulations in whole navigation risk management process within the port area. Today’s port regulations are created mostly based on good practice of pilots and experts, whereas the quantitative methods are used less frequently. The intention of the presented case study was to demonstrate how the quantitative risk assessment could be used in port policy development.