Exploration for submerged prehistoric archaeological sites in the Great Lakes (North America) is a major challenge due to difficulties in locating scant cultural artifacts in lake-bottom sediments. Stone tool microfragments (microdebitage, <1 mm) can be abundant (>106 per tool) and more dispersed around tool-making sites, but have not been identified previously in an underwater context. To evaluate their use as a submerged site indicator, microdebitage analysis was conducted on five lake sediment cores from a shallow lagoon adjacent to a long-occupied prehistoric site (McIntyre site, Rice Lake, Ontario). We identified 155 microdebitage fragments within a distinctive muddy peat horizon (2–2.5 m depth) using light microscopy and scanning electron microscopy methods. The microdebitage consisted of angular to very angular quartz fragments (400–1000 μm) with characteristic conchoidal fractures and flake scars produced by mechanical percussion. The microdebitage horizon had a distinctive bimodal particle size peak and contained a low-diversity soil thecamoebian assemblage (Phryaginella, Bullinularia sp.) indicative of a wetland environment that formed during an early Holocene shoreline transgression. Accelerator mass spectrometry 14C dating of wood fragments yielded ages of 9470–8760 ± 50 yr B.P. (11,070–9560 cal [calibrated] yr B.P.), indicating a Late Paleoindian–Early Archaic age for the deposit. Results demonstrate that coring and microdebitage analysis are effective tools in the search for underwater prehistoric sites and can be employed more broadly in exploration of submerged landscapes in the Great Lakes basins.