Piston cores from deep-water bottom deposits in Lake Ontario contain shallow-water sediments such as, shell-rich sand and silt, marl, gyttja, and formerly exposed shore deposits including woody detritus, peat, sand and gravel, that are indicative of past periods of significantly lower water levels. These and other water-level indicators such as changes in rates of sedimentation, mollusc shells, pollen, and plant macrofossils were integrated to derive a new water-level history for Lake Ontario basin using an empirical model of isostatic adjustment for the Great Lakes basin to restore dated remnants of former lake levels to their original elevations. The earliest dated low-level feature is the Grimsby-Oakville bar which was constructed in the western end of the lake during a near stillstand at 11-10.4 (12.9-12.3 cal) ka BP when Early Lake Ontario was confluent with the Champlain Sea. Rising Lake Ontario basin outlet sills, a consequence of differential isostatic rebound, severed the connection with Champlain Sea and, in combination with the switch of inflowing Lake Algonquin drainage northward to Ottawa River valley via outlets near North Bay and an early Holocene dry climate with enhanced evaporation, forced Lake Ontario into a basin-wide lowstand between 10.4 and 7.5 (12.3 and 8.3 cal) ka BP. During this time, Lake Ontario operated as a closed basin with no outlets, and sites such as Hamilton Harbour, Bay of Quinte, Henderson Harbor, and a site near Amherst Island existed as small isolated basins above the main lake characterized by shallow-water, lagoonal or marsh deposits and fossils indicative of littoral habitats and newly exposed mudflats. Rising lake levels resulting from increased atmospheric water supply brought Lake Ontario above the outlet sills into an open, overflowing state ending the closed phase of the lake by *7.5 (8.3 cal) ka BP. Lake levels continued to rise steadily above the Thousand Islands sill through mid-to-late Holocene time culminating at the level of modern Lake Ontario. The early and middle Holocene lake-level changes are supported by temperature and precipitation trends derived from pollen-climate transfer functions applied to Roblin Lake on the north side of Lake Ontario.Electronic supplementary material The online version of this article (