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This paper introduces a new simulative approach to assess the level of underwater security in civilian harbor installations, with the aim of bridging the gaps between system specifications and operative performance of anti-intrusion systems. The integration of a geographical information system (GIS), acoustic and magnetic sensor models, with a dynamic simulator makes it possible to simulate the impact of both new sensors and modification in the sensors placement in the overall harbor protection system. With the proposed approach it is possible to model the harbor environment including geographical and environmental information, to set up the surveillance system with underwater acoustic and magnetic sensors and reacquisition vehicles, and to add several types of intruders to estimate, through dynamic simulations, what security level is obtained by the sensors configuration chosen against the selected intruder. The intention is that of hiding the physical aspects of acoustic and magnetic propagation while providing high-level figures of merit (probability to stop the intruder, expected halt distance from the high value asset (HVA), and expect halt time to intercept) capable of a clear representation of the system capability to detect, classify, and stop a menace. For this purpose, a software simulator tool has been developed and its usage in several scenarios has been reported (e.g., sensors configuration and deployment, performance sensitivity to changing oceanic conditions).