Due to the increasing ship traffic flow in ports, maritime traffic safety has attracted much attention. In addition to traffic flow, the ship safety in restricted waters is influenced by external navigational factors (visibility, wind and current), encounter situations and human factors on board. In this paper, we investigate the effect of navigational factors on ship behavior. The raw AIS data and locally measured visibility, wind, and current data in the port of Rotterdam are collected to investigate the impacts of wind and current on ship speed and path (distance to the starboard bank). The results reveal that the wind mainly affects the paths of ships by the force of cross-wind, while the current impacts the speed over ground of ships when the current is with or against the heading of ship. The impacts on different sizes of ships are different as well. The port side wind has a larger impact on small ships than on large ships, while the impact of starboard side wind is larger for large ships than for small ships. The impact of current on the speed over ground is larger on small ships than large ships, and least on medium ships. The analysis results could assist the port authority in predicting ship traffic in different situations, and be used in the development of a new maritime traffic model to simulate ship behavior while considering the external navigational factors.