This paper evaluates near ship-ship collision situations in the Tagus River Estuary using a simulation model of ship navigation in restricted waters. The simulation model consists of a ship collision avoidance model based on the Artificial Potential Field (APF) method, which has been improved to account for the lateral distribution of traffic along the route, the ship type and length and speed development of the ships along the trajectory. AIS data of ships entering and leaving the port of Lisbon are analysed to obtain the main characteristics of traffic parameters used as input for the traffic simulation model, such as: the routes of the vessels, speed distribution along the routes, traffic density and characteristics of the ships in each route, among others. First, the improved model of ship navigation and the Monte Carlo simulation technique are used to simulate the marine traffic in the Tagus River Estuary. Then, the concept of “ship domain” is used as collision criterion to determine the number of near collisions and the locations where they are most likely to occur. Finally, the simulation results are compared to the ones obtained from raw AIS data to assess the capability of the simulation model for marine traffic risk analysis.