This article describes research aimed at developing a system able to support local authorities and port communities in optimizing port navigation, avoiding or managing critical situations induced by sea-level variations in harbours and minimizing environmental damages and economic losses. In the Mediterranean basin, sea-level changes are mostly due to astronomical tides, related to the gravitational attraction between Earth, Moon and Sun. Nevertheless, sea-level variations are also influenced by meteorological tides, which are geodetic adjustments of sea surface due to atmospheric pressure variations above a water basin. So, starting from monitoring or forecasting environmental parameters in harbours, the system updates port bathymetric maps based on sea-level variations (acquired in the past, measured in real-time, or expected in the future) and detects hazardous areas for a certain ship moving inside a port at a given moment, by means of the implementation of “virtual traffic lights”. The system was tested on some real situations, including the analysis of maritime accidents (stranding of ships), providing satisfactory results by correctly signalling potentially dangerous areas variable over time. The architecture of the system and results achieved using it in the ports of Livorno and Bari, in Italy, are herewith described.