Context: From the perspective of marine traffic engineering, a system of port waterways is composed of a set of waterways (port areas), such as approach channels, port entrance, inner fairways (port channels, rivers, lakes), turning basins and port basins of various terminals. The sea waterway must be adjusted to the navigation of specific types of ships, characterized by length, breadth, draft and airdraft. The primary requirement for shipping in sea waterways is the safety of navigation. Each sea waterway has traffic restrictions for the ships using it. These restrictions are called conditions of sea waterway operation or conditions of ship operation in the sea waterway. Problem: There are a number of empirical, deterministic or probabilistic methods to determine the safe width of maneuvering areas on port waterways. The direct application of empirical methods to determine the conditions for the safe operation of ships on the complex waterway, such as the Świnoujście–Szczecin fairway, was impossible due to the complexity of the waterway and various restrictions on its individual parts. Method: The paper presents the assumptions and calculation procedure of a method allowing for the determination of maximum safe parameters of ships in existing complex waterways. Results: The proposed method was used in the preparation of port regulations for the dredged and widened Świnoujście–Szczecin waterway. The results of these calculations are presented as a practical application of the method. Conclusions: This article defines conditions for the safe operation of ships in complex port waterways systems and presents the methodology for determining maximum safe parameters of ships in existing complex port waterways systems.