The early to middle Holocene was marked by considerable variability in lake levels in the Lake Superior Basin due to a combination of meltwater runoff, isostatic adjustment, shifting glacial margins, and climate change. These processes likely had a large impact on the preservation and visibility of coastal archaeological sites dating from the Early Period (Paleoindian) to the Middle Period (Shield Archaic). Of particular interest is the brief interval after 9300 cal. B.P. when ancestral Lake Superior dropped to its lowest level (Houghton) and human populations may have made incursions deeper into the basin. Elsewhere in the Upper Great Lakes, this period is associated with offshore archaeological sites submerged by rising water levels later in the Holocene. New geological data from the Thunder Bay, ON, region yield exceptional insight into the paleohydrology of the Houghton phase and, hence, the underwater archaeological prospects of this low water phase in the northern Lake Superior Basin. These data indicate that the lake reached its lowest level by at least ~9100 cal. B.P. but was highly unstable, at least initially, due to a combination of climate and meltwater runoff. Early underwater sites may be confined to two short, hydrologically closed, lowstands between ~9100 and 8700 cal. B.P. and would have been impacted by at least one lake transgression. Such sites, however, may still hold better potential for organic preservation and the visibility of large cultural features compared to their terrestrial counterparts. Coastal sites occupied when the lake was hydrologically closed may be especially well‐preserved due to rapid inundation before the gradual, and generally erosional, Nipissing transgression occurred.