Accidents in port areas are generally relatively minor given the lower prevailing speeds, but dangerous cargo terminals located in the vicinity of populated areas present some risk of accidents with catastrophic consequences. The maritime risk assessment frameworks have been developed in many ports, but few include studies incorporating collisions between sailing and moored ships. This paper presents the risk assessment framework for such accidents. Moreover, it presents the important role of harbour regulations in the navigation risk management process within the port area. Today’s port regulations are created mostly based on the good practice of pilots and other experts, whereas quantitative methods are used less frequently. The intention of the presented case study was to demonstrate how quantitative risk assessment may be used in port policy development, which is why the method created is general and may be used in any terminal with dangerous cargo. The multi-stage method consists of several steps that make up a complex methodology, consisting of expert study, real-time simulation—a simulation of a collision in port is presented—and analytical-empirical calculations for consequence assessment. The case studies of the developed method are presented based on two real accidents, one in the Police port along the Świnoujście-Szczecin waterway, and the second in the Port of Koper in Slovenia. The results of this study present the parameters of the ship’s safe approach to the terminal area, such as velocity and approaching angle. These parameters are used to calculate the impact forces in the case of a collision between a moored and passing ship and its consequences on ship integrity as well as on mooring arrangement. Based on probability and consequences, the risk is evaluated and discussed in the sense of port safety. The presented method could be used as the framework for risk assessment of collisions in a port area, particularly when dealing with dangerous cargo or sensitive vessels such as cruise ships.