Traditional naval vessels with steel structures have the benefit of large safety factors and a distinct material endurance limit. However, as performance requirements and budget constraints rise, the demand for lighter weight vessels increases. Reducing the mass of vessels is commonly achieved by the use of aluminum or composite structures, which requires closer attention to be paid to crack initiation and propagation. It is rarely feasible to require a lengthy inspection process that removes the vessel from service for an extended amount of time. Structural health monitoring (SHM), involving continuous measurement of the structural response to an energy source, has been proposed as a step towards condition-based maintenance. Furthermore, using a passive monitoring system with an array of sensors has several advantages: monitoring can take place in real-time using only ambient noise vibrations and neither deployment of an active source nor visual access to the inspected areas are required. Passive SHM on a naval vessel is not without challenge. The structures of ships are typically geometrically complex, causing scattering, multiple reflections, and mode conversion of the propagating waves in the vessel. And rather than a distinct and predictable input produced by controlled active sources, the vibration sources are hull impacts, smaller waves, and even onboard machinery and activity. This research summarizes findings from data collected onboard a Navy vessel and presents recommendations data processing techniques. The intent is to present a robust method of passive structural health monitoring for such a vessel using only ambient vibrations recordings.