Hamilton Harbour, which was once Burlington Bay, lies on the western tip of Lake Ontario, bounded on the northwest by the City of Burlington, on the south by the City of Hamilton, and on the east by Hamilton Beach (south of the Burlington Bay James N. Allan Skyway) and Burlington Beach (north of the channel). It is joined to Cootes Paradise by a narrow channel formerly excavated for the Desjardins Canal. Within Hamilton itself, it is referred to as Hamilton Harbour, the Harbour and the Bay, but never Burlington Bay. The bay is naturally separated from Lake Ontario by a sand bar. The opening in the north end was filled in and channel cut in the middle for ships to pass.
The bay was named in 1792 by John Graves Simcoe, the first lieutenant governor of Upper Canada, for the former name of the town of Bridlington in the East Riding of Yorkshire, England. Access to the bay was important for the early water transportation and industrial development of the area, including Dundas, Ontario, which had an early but ultimately unrealized lead over both Burlington (Brant's Block) and Hamilton.
Over the years, the bay was roughly treated by its littoral residents. Constant infilling, particularly in the North End of Hamilton, damaged fresh water streams and the wildlife they supported. Channel dredging tended to stir up natural and unnatural sediments, further disrupting the ecological land balance in the area. Chemical, industrial and thermal pollution, especially as a byproduct of the burgeoning steel industry after the 1890s, continued to degrade the environment.
In 1919, a Federal Order-In-Council changed the name of Burlington Bay to Hamilton Harbour.
By the 1970s, the International Joint Commission, which governs water usage in the Great Lakes Basin, and other agencies began to recognize the need for action. Greater water quality awareness, improved pollution controls, and an economic downturn all served to improve conditions in the 1980s. In the 1990s, beautification and ecological control were well underway. These measures included sealing the Lax Lands, contaminated with heavy metals and other pollutants, under a cap of clay; landscaping Bayfront Park and Pier 4 Park; and keeping Asian carp from entering Cootes Paradise. The visible and measurable improvement in water quality in Burlington Bay was showcased in 1994 by the very public swim of Sheila Copps, a local MP and federal cabinet minister. Access and recreational use of the bayfront has improved, and swimming is now allowed at two beaches in the harbour - Bayfront and Pier 4. 
Hamilton Harbour is listed as a Great Lakes Areas of Concern in The Great Lakes Water Quality Agreement between the United States and Canada. Part of the remediation plan is to reclaim the harbour's wetlands.
The bay is thought by some to host a North American cryptid, described by witnesses as a large snake-like creature. A diver drowned in the bay during the filming of a low-budget horror film titled Marina Monster on August 21, 2005.
- Houghton, Margaret (2002). Hamilton Street Names: An Illustrated Guide. James Lorimer & Co. Ltd. ISBN 1-55028-773-7.
- Rayburn, Alan Place Names of Ontario (University of Toronto Press), Toronto-Buffalo-London,1997, ISBN 0-8020-7207-0), pg.48
- Politicians answered dare to swim in Burlington Bay Hamilton Spectator, August 16, 2006
- Hamilton Harbour AOC Remedial Action Plan, Environment Canada
- Great Lakes Wetlands Conservation Action Plan, Environment Canada contains five paragraphs about the harbour project
- At Last, Clean Water, National Post, November 13, 2007
- Cleaning Up Randle Reef In Hamilton Harbour - Part of the Government of Canada's Action Plan for Clean Water, Environment Canada, 2007-11-09
- The Kingston Daily News, August 17, 1877, Great Lakes Newspaper Transcriptions
- Diver Drowns on Low-Budget Film Shoot in Hamilton Harbour, CBC News, August 22, 2005