Toronto Harbour is a bay on the north shore of Lake Ontario. Originally a low sandy peninsula formed the southern limit of the bay. The mouth of the harbour pointed west. The eastern shore of the bay, approximately six kilometres east, was a marsh around the mouth of the Don River. Low sandy bluffs lined the northern shore.

In 1858 a storm washed a channel through the eastern edge of the peninsula that formed the south edge of the bay, forming the Toronto Islands.

As the city of Toronto grew the northern shore of the bay has been altered by landfill, and has been moved approximately 500 meters south. In addition to the Don River a number of smaller creeks flowed into the bay.

The original site of the town of York had half a dozen short creeks that flowed through it. As the town developed they all became polluted, and were buried. As the city grew the larger two creeks, Taddle Creek and Garrison Creek, were also filled in.

The Scarborough Bluffs are much larger bluffs that lie approximately ten kilometres east of the harbour. Currents washed the sand eroded from the bluffs westwards to form the bay.

Fort York, on the north shore of the bay, near the mouth of Garrison Creek, guarded the harbour's mouth. It was briefly captured by American forces during the War of 1812.

Toronto Harbour is both a commercial port and a recreation area. Commercial activities are confined mainly to the harbour's eastern side, while the western side has been developed into Harbourfront, a project designed to afford people access to their once forbidding, industrialized harbour. Harbourfront now has parks, hotels, an amphitheatre, and many other facilities. The Toronto Islands are also mostly recreational, although they do also contain a small community and an airport.

Toronto also has a second harbour, called the Outer Harbour (Toronto Harbour is sometimes called the Inner Harbour), but it never developed into a commercially viable project. It was created in the 1950s by the Toronto Harbour Commission through the construction of a new breakwater called the Outer Harbour East Headland. At that time, it was expected that there would be a great upswing in the number of ships calling at Toronto once the Saint Lawrence Seaway opened. However, the need for an extra harbour never materialized, and private boats are the only traffic usually found there now.