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Abstract For much of modern human history (roughly the last 200,000 years), global sea levels have been lower than present. As such, it is hardly surprising that archaeologists increasingly are looking to submarine environments to address some of their most pressing questions. While underwater archaeology is most commonly associated with shipwrecks, the search for submerged prehistoric sites presents an entirely different set of challenges, even though many of the same technologies are used. For Great Lakes archaeologists, the problem is how best to adapt the range of available seafloor mapping and testing techniques to the problem of identifying prehistoric sites, while operating with smaller vessels and the limited budgets available to “normal” archaeology. In this paper, we briefly describe the approach we have developed at the University of Michigan for identifying 9,000-year-old caribou hunting sites beneath Lake Huron. The research employs a layered research design integrating sonars, remotely operated vehicles (ROVs), and scuba divers at progressively finer scales to discover and investigate these important new archaeological sites.