[1] It was first located in the historic Stanley Barracks' Officers' Quarters on the grounds of the Canadian National Exhibition.

In 1964, it was proposed to display a selection of historic ships: the PS Trillium former island ferry, the Venetia a Chinese trader, the G. R. Geary steam tug, the Naiad yacht, and the St. Lawrence, a 100-gun gunboat that was sunk in Kingston, Ontario's harbour.

Although not related to the museum's purpose, ex-CN Rail / Canadian Northern Railway locomotive 6213 was stored outside.

In 2000, the museum was moved to Pier 4 at 245 Queens Quay West at a former warehouse (c. 1930s), which is closer to downtown, and more accessible for tourists.

The Harbourfront building was repurposed for a pet activity centre and is currently a craft beer store and restaurant.