Hamilton Harbour is a naturally protected body of water that was created during the last glaciation period. Its watershed comprises an area of 500 square kilometers which is encompassed by a shoreline measuring 45 kilometers in length. The harbour is accessible from Lake Ontario through a short channel known as the Burlington Shipping Canal.
The Niagara Escarpment surrounds the Harbour on three sides (the fourth is formed by Lake Ontario) and its streams create numerous spectacular waterfalls. Three streams in particular, with their headwaters above the Escarpment, feed into the Harbour: Grindstone Creek drains the north central area of the watershed; Red Hill Creek drains the southeast sector of the basin; and Spencer Creek drains the northwest and western parts of the watershed. The conservation authority of Hamilton Harbour is the Hamilton Conservation Authority.
While the Harbour itself is governed by the Hamilton Port Authority, the relevant municipalities are the Cities of Hamilton and Burlington, the Region of Halton, and the Township of Puslinch. These jurisdictions extend from the shoreline to the major hinterlands of the Niagara Escarpment.
As one of the 43 Areas of Concern identified by the International Joint Commission under the Great Lakes Water Quality Agreement (1987 revised protocol), the harbour is recognized as chronically degraded. The impairments to Hamilton Harbour include: point–source pollution (sewage–treatment plants, industry), non–point source pollution (runoff from urban and rural areas), contaminated sediments from heavy industry, combined sewer overflows, shoreline development, increasing development in the watershed in general, and the impact of invasive non–native species such as carp.