Construction of new ports requires applying the entire range of methods and the close cooperation between designers and specialists of different field including safety of navigation or oceanography. At present there is no possible to conduct of such investments without carrying out simulation examinations. These studies most often take place as multistage where the next stage is the result of the previous one. The paper presents complex method of water areas optimization with consideration of navigational safety. In the present study was implemented real-time simulation method. Methods of the simulation of the real time leaning against manoeuvre simulators have been applied. Two distinct from each other alternatives have been explored and the best in terms of safety of navigation has been selected as final. The results were used as a guideline for the development project of a small Polish seaport in Mielno.