Between 10,500 and 9000 cal yr BP, δ18O values of benthic ostracodes within glaciolacustrine varves from Lake Superior range from − 18 to − 22‰ PDB. In contrast, coeval ostracode and bivalve records from the Lake Huron and Lake Michigan basins are characterized by extreme δ18O variations, ranging from values that reflect a source that is primarily glacial (∼ − 20‰ PDB) to much higher values characteristic of a regional meteoric source (∼ − 5‰ PDB). Re-evaluated age models for the Huron and Michigan records yield a more consistent δ18O stratigraphy. The striking feature of these records is a sharp drop in δ18O values between 9400 and 9000 cal yr BP. In the Huron basin, this low δ18O excursion was ascribed to the late Stanley lowstand, and in the Lake Michigan basin to Lake Agassiz flooding. Catastrophic flooding from Lake Agassiz is likely, but a second possibility is that the low δ18O excursion records the switching of overflow from the Lake Superior basin from an undocumented northern outlet back into the Great Lakes basin. Quantifying freshwater fluxes for this system remains difficult because the benthic ostracodes in the glaciolacustrine varves of Lake Superior and Lake Agassiz may not record the average δ18O value of surface water.