Before the building of bridges, punts facilitated traffic across the Yarra River. The best-known were at the site of the present Princes, Punt Road and Hawthorn bridges. The first rope-hauled punt, on the site of Princes Bridge, was operated by William Watts from 1838. James Palmer's punt at Hawthorn operated from 1842, and a rival punt ran nearby. Several other punts operated on the river in the city area from the 1840s. Two other points were of sufficient importance to warrant steam punts. The first of these, between Spencer Street and Clarendon Street, the site of the present Spencer Street (Batman) Bridge, operated from 1884 until the late 1920s. The most recent was from Williamstown Road, Port Melbourne, to a point by Newport power station. Three steam-powered punts, each larger than its predecessor, ran here between 1873 and 1974, and were guided across the river on a chain. The last, with a capacity of 32 vehicles, was built in 1931.
Early punts, as described by 'Garryowen' (in The chronicles of early Melbourne), comprised a 'dray without wheels, made water-tight by tarpaulin ... launched through the agency of a small rope looped round the main rope across the river'. In 1839 William Lonsdale set the site of a punt servicing the road from Williamstown to Geelong on the Saltwater (Maribyrnong) River, a little above its junction with the Yarra at the site of present-day Footscray. First operated by William Watts, the punt was taken over in 1840 by Benjamin Levien in association with his Victoria Hotel on the western bank of the river. The original punt could only bear two horses or a light cart, but with the increased traffic of mail carts, coaches and other private conveyances, Levien constructed a new punt with improved capacity and lanterns for night crossings.
Steam ferries commenced service from the Yarra to Williamstown before the building of the railway, and another ran upstream from Princes Bridge to Cremorne Gardens. The Fire Fly ran the first ferry service on the Yarra on 28 October 1838. Ferries met the Geelong trains at Greenwich Point for two years before the completion of the line to Spencer Street.
A service of greater significance was provided between Port Melbourne and Williamstown, principally by the paddle steamer Gem, which gave its name to Gem Pier. The Gem, under Captain Robert Watson, plied across Hobsons Bay from 1868 until 1911, and connected directly with the Port Melbourne railway. The Rosny, the last ferry boat on the service, operated between 1919 and 1931. Other ferries in service on this run were the Queen and Baldrock (1907-11), and Planet and Williamstown (1910-19).
Several smaller cross-river services have also been run in the port area with rowing boats and later with motor boats, the last of which, from Spotswood to Fishermans Bend, closed in 1979. Regular services between the Yarra (Southbank) and Williamstown were reintroduced in the 1990s, as well as a weekend ferry from St Kilda Pier to Williamstown, begun by the John Batman in 1986.