The Harbour Commission was the third organization to manage the Port of Toronto, after the Commissioners of the Harbour of Toronto, known as the Harbour Trust, formed in 1850. Prior to 1850, the harbour had had three commissioners appointed by the province of Upper Canada to oversee harbour works, in conjunction with the building of the Queen's Wharf, at the foot of Bathurst Street in 1833. One of the commissioners, Hugh Richardson, was named Toronto's first Harbourmaster in 1837 and he imposed wharf fees to pay for the Wharf.
The Harbour Trust was formed in 1850 at the suggestion of the Toronto Board of Trade. On behalf of port users, the Board expressed complaints in the operation of the provincial commission, which made no improvements in the harbour. The harbour was beset by silting problems which needed to be rectified. This second commission was governed by a five-man board, two from the City of Toronto, two from the Board of Trade and a fifth appointed by the province of Upper Canada, nominated by the four other members.
The Harbour Trust was also given authority over the Esplanade plan. The original 1817 plan intended to build a public walk and garden along the waterfront, just south of Front Street. The province's plan was largely ignored and the City allowed the use of the shore line to be used for wharves and docking. In 1837, a new plan was developed for the Esplanade. In this plan, the Esplanade would be built just south of Front, and the waterfront extended south to the "Windmill Line", some 100 yards south. The new lands would be used for port uses. The Esplanade itself would become mostly railway lands.
The intrusion of the railways into the waterfront in the 1850s to 1890s period started to crowd out recreational uses. In 1892, a legal agreement solidified the railways usage of the waterfront. In 1893, a new plan was developed to extend landfill another 600 feet (180 m) south, and a new Lake Street (today's Lake Shore Boulevard) established along the then current waterfront edge. The problem of silting, and the increasing amount of sewage being dumped in the harbour, required ongoing dredging efforts. Other works by the Harbour Trust including a breakwater at the Don River and a breakwater at the Queen's Wharf to protect the entrance to the harbour.
The wetlands of the Don River were becoming increasingly polluted. Plans were developed to convert the area (1,000 acres in size) into usable lands. A planning advocacy group, the Civic Guild unveiled a plan in 1909 which advocated industrial and recreational uses for the land. The Board of Trade advocated the reclamation and infilling of the wetlands for port and industrial uses. The existing port facilities were inadequate when a railway strike occurred in 1910, forcing vessels to wait days to dock.