A deep channel in bedrock extending to more than 25 m below sea level occurs along the north shore of the otherwise uniformly shallow Kingston basin of Lake Ontario. Bathymetric and subbottom acoustic data are used to map the topography of the channel and to reconstruct its late glacial and postglacial sedimentary history. The results are interpreted as showing that the large channel and smaller channels nearby were created by high-velocity subglacial meltwater flow. Acoustic facies assemblages of sediments deposited in the channels record patchy deposition, or deposition followed by partial erosion, of glacial sediments on the bedrock of the channel floor, followed by deposition and episodic erosion of glaciolacustrine sediment in a high-energy, ice-proximal lake. Palaeoslope analysis confirms that the early Holocene low-water phase of Lake Ontario resulted in the development of a fluvial system in part of the channel. Water level was controlled by a sill at Kingston. Kingston basin, the Bay of Quinte, and possibly, for a short time, a much larger area of the upper Great Lakes drained through the channel. However, for most of the period, until it was flooded by the rising waters of Lake Ontario, the channel was occupied by a small river on a wide floodplain or it was flanked by broad marshes.