Bateau Channel is the smallest and most northerly of the three outlets of Lake Ontario. Near its narrowest point (125 m at present water level) it is 60 m deep, making it one of the deepest places in eastern Lake Ontario. Evidence is presented to show that the trench formed as a result of high-velocity subglacial meltwater flow over a scarp at the boundary of the Precambrian Shield and Ordovician limestones to the southeast, and concentrated along a glacial or preglacial depression. Similar trenches occur across this boundary to the northwest. During flooding by Lake Iroquois, the trench was partially filled with glacilacustrine sediment. During the low-level phase of early Lake Ontario, the channel was abandoned and subaerially exposed. Calculations based on the slopes of the isostatic surface and of Bateau Channel suggest that it was reinundated about 7 ka BP and parts of the trench were exhumed to bedrock. Shell fragments 1.7 m below the sediment surface in a core recovered from marly sediment forming a shelf along the channel sides dated at 3440 ± 80 BP (TO-1587), indicating that deposition of this shelf occurred during recent rising water levels.