The Homeland Defense community is increasing its focus on port security and harbor protection. Rising to the challenge, the U.S. Coast Guard is tasked with monitoring and protecting our harbors where commercial container ships enter. Tracking of the onboard containers is of great concern to the protectors of the waterfront. A system capable of identifying the number of containers onboard the vessel, when the containers are added or removed, contents of the containers, etc., will significantly reduce the potential for a security problem by providing essential information to the Coast Guard or other port security so that they can decide whether or not pre-boarding is necessary. That is, boarding the ship and inspecting the cargo while still at a safe distance from the harbor. A conceptual pictorial of this concept is shown in Figure 1. This paper presents a system that utilizes transmitters embedded on the containers which incorporate unique ID codes identifying the container, its history, and other information. A Communication/Navigation Aid (C/NA) type vehicle/buoy concept, presently being developed by Sippican (under contract to the Office of Naval Research (ONR) as part of the Autonomous Operations -- Future Naval Capabilities (AO-FNC) program, positioned at sea, would include a payload of NuWaves’ communication transceivers able to receive the cargo container’s transmitted ID and forward this information by RF link to a ground station. The Port Authority and/or the Coast Guard would then utilize the information to make an assessment of the vessel prior to port entry. Although, this paper illustrates a scenario applicable to the cargo shipping industry, it is also applicable to other homeland defense areas such as unattended open ocean force protection, drug and law enforcement, and environmental monitoring.