Methods and apparatus determine if an intruder passes into a security zone that is associated with a waterfront asset. An embodiment of the invention provides a harbor fence system that is designed to be deployed in water around ships or other waterfront assets to serve as a line-of-demarcation in order to provide protection. The harbor fence system comprises a series of spars that protrude above the water surface and that are connected with an electrical computer with a telemetry subsystem. Each spar contains electronic sensors, e.g. water immersion sensors and accelerometers, and circuitry to detect an intrusion and to communicate the location of the intrusion to a computer control station. The embodiment also facilitates deploying and retrieving the harbor fence system. Additionally, the embodiment may also determine whether an underwater intruder is passing under a protective boundary, in which the harbor fence system interfaces to an underwater sonar sensor subsystem.