The first wharves on the Yarra River were located as close as possible to the city. From 1835 vessels were moored directly to the bank or to stakes driven into the river. An 1839 wharf plan foundered on the unavailability of convict labour so the first wharf was built by Captain George Cole in 1841. Cole's Wharf, between King and Spencer streets, near the Customs House, was a busy centre for steamer traffic where cargo could be loaded directly from the ships to wagons on the quay. The south bank river frontage was leased for shipping and related uses from the 1850s. On the site of the present Crown Entertainment Complex was, from the 1870s, a stone quay with a steam crane. The piecemeal development of the port proved unsatisfactory and a royal commission into the establishment of a port authority took place in 1860. By this time there were river wharves for 36 vessels compared with berths at piers at Williamstown and Sandridge for 43.
Following the establishment of the Melbourne Harbor Trust in 1877, improvements were set in hand resulting in the completion of the Fishermans Bend Cut (Coode Canal) in 1886 and the West Melbourne (Victoria) Dock in 1892. New wharves had been completed by 1903. Victoria Dock, whose central pier was built about 1916, had 21 berths and was the principal overseas cargo terminal in the 1930s. During the visit of the American fleet in 1925 it was host to a cruiser, 24 destroyers and two depot ships. It is now given over to housing and recreational uses. The increasing size of ships forced development in the lower river, the building of new swinging basins and the reclamation of flood-prone land for wharves. The Appleton Dock was commenced in 1913 but remained only partly complete in 1956 and further development was proposed in 2004. During the 1930s some 2.7 km of berthing was constructed at South Wharf.
Among various specialist berths there have been coal, bulk sugar, ammonia, cement, gypsum and phosphate wharves, and timber and oil wharves. Coode Island, despite fires in 1991, retains bulk chemical facilities.
The building of the Spencer Street (Batman) Bridge in 1927 cut off the river wharves upstream, and the river has been further cut off from shipping subsequently by the Charles Grimes Bridge in 1975 and the Bolte Bridge in 1998. Little Dock (originally New Dock, then Spencer Dock) on the site of the present Melbourne Convention Centre, was used by local sailing vessels from 1854 to 1930 and was convenient to the metropolitan fish markets.
Relics of the older style of cargo handling are the wharf sheds associated with the Melbourne Maritime Museum and adjacent businesses. The wharf and the dock sheds at Nos 5 to 9 (formerly Nos 13 to 17) South Wharf were built between 1885 and 1929 and the former No. 2 (ex No. 10) shed, now relocated in the museum, was constructed in 1891. Dock sheds of this kind were made redundant by the need for large areas of open space for the storage and sorting of shipping containers, and for the marshalling of vehicles.
Changes in types of ships also brought new dock development. The 'roll-on-roll-off' vessels such as the Princess of Tasmania used Webb Dock at Port Melbourne from 1959, and the first container berths in the new Swanson Dock commenced work in 1969. Containerisation was a shipping revolution and the commitment of the Port of Melbourne to early handling of container cargoes gave it a significant edge in the national shipping trades. It could boast of being the largest cargo port in the southern hemisphere and the largest container port in Australia. It has been ranked as 27th in the world among ports for container throughput. Trade continues to increase and Melbourne also serves the majority of overseas container cargoes for Tasmania and South Australia. In a typical year up to 24.7 million tonnes of cargo pass through Melbourne. Swanson Dock was completed with a guaranteed depth of 10.9 m but deepening will allow the berthing of ships up to 14 m draft. Since the cutting off of Victoria Dock by the Bolte Bridge, Webb Dock has been extended for container traffic.
Several dry docks for the refit and repair of ships have existed on the Yarra. Hughes & Sinnott's Dock, excavated in 1868, was the source of some dispute when efforts were made to widen the Yarra around it in 1878 and there was a virtual battle between the dock owners and the Harbor Trust. Wright & Orr Co.'s new dock was used from 1878 to 1932 and some of its entrance is still visible. As extended in 1907 it measured 420 feet in length (128 m), 52 feet (16 m) across the entrance and 23 feet 6 inches (7 m) deep at high tide. Duke's Dock was next to it downstream, built first in 1875, extended in 1880 and rebuilt in 1901-04. It was then the largest in Victoria, with minimum dimensions after extension in 1935 of 527 feet (160 m) length, 61 feet (19 m) across the entrance and 23 feet 6 inches (7 m) deep at high tide. Docking of large ships here might see their bowsprits hanging over Normanby Road. The largest ship to be docked here was 10 000-ton Commissaire Ramel in 1931 and the longest the 500-feet (152-m) City of Dieppe in 1947. During World War II it was very busy, with 74 ships docked in a year. Sometimes two vessels might be docked at the same time. It was closed in 1975 and passed to the National Trust who maintain it, though it is now partly filled with the museum ship Polly Woodside. It is a rare example of a timber-framed graving dock, the construction necessitated by the swampy nature of the site. This last dock was replaced by the floating drydock A. J. Wagglen, with a lift of 8000 tonnes, in 1975. When this dock was taken away in 1993 the port of Melbourne lost a major facility in commercial ship repair and maintenance. The dry docks in the Yarra were supplemented by the Alfred Graving Dock and a series of small floating docks at Williamstown.