The harbour is called Jipugtug by the Mi'kmaq first nation, anglicized as Chebucto. It runs in a northwest-southeast direction.
Based on average vessel speeds, the harbour is strategically located approximately one hour's sailing time north of the Great Circle Route between the Eastern Seaboard and Europe. As such, it is the first inbound and last outbound port of call in eastern North America with transcontinental rail connections.
The harbour is largely formed by a drowned glacial valley which succumbed to sea level rise since glaciation. The Sackville River now empties into the upper end of the harbour in Bedford Basin; however, its original river bed has been charted by the Canadian Hydrographic Service throughout the length of the harbour and beyond.
The harbour includes the following geographic areas:
- Northwest Arm: Another drowned river valley now largely used by pleasure boats.
The Narrows: A constricted passage to Bedford Basin.
- Bedford Basin: A sheltered bay and the largest part of the harbour.
The harbour is home to several small islands.
The harbour limit is actually formed by the northern end of its largest island - McNabs Island. The largest island entirely within the harbour limits is Georges Island, a glacial drumlin similar to its dryland counterpart at Citadel Hill. Several small islands are located in the Bedford Basin near Bedford and Burnside.
In the Northwest Arm, there is a small peninsula known as Deadman's Island, named for the burial location of War of 1812 prisoners of war. Just 200 m west of Deadman's Island is the equally small Melville Island, which is connected to the mainland by road. Melville Island forms the eastern boundary of Melville Cove and is also the location of the Armdale Yacht Club. Melville Cove is also the name of the adjacent residential community.
Although outside the defined harbour limits, Lawlor Island and Devils Island are also frequently included in descriptions of Halifax Harbour and the surrounding area.