This paper presents an autonomous robot system that is designed to autonomously search for and geo-localize potential underwater archaeological sites. The system, based on Autonomous Underwater Vehicles, invokes a multi-step pipeline. First, the AUV constructs a high altitude scan over a large area to collect low-resolution side scan sonar data. Second, image processing software is employed to automatically detect and identify potential sites of interest. Third, a ranking algorithm assigns importance scores to each site. Fourth, an AUV path planner is used to plan a time-limited path that visits sites with a high importance at a low altitude to acquire high-resolution sonar data. Last, the AUV is deployed to follow this path. This system was implemented and evaluated during an archaeological survey located along the coast of Malta. These experiments demonstrated that the system is able to identify valuable archaeological sites accurately and efficiently in a large previously unsurveyed area. Also, the planned missions led to the discovery of a historical plane wreck whose location was previously unknown.