The Inner Harbour, adjacent to the historic city of Fremantle, provides facilities for handling container trade, break bulk vessels, livestock exports and motor vehicle imports. It also accommodates cruise ships and visiting naval vessels.

The Inner Harbour comprises three main areas: North Quay, Victoria Quay and Rous Head.

North Quay accommodates the Port's two container terminals, which occupy the greater proportion of the Quay, and a number of general cargo berths used mainly for break bulk and liquid bulk cargoes.

Victoria Quay has two main areas: the eastern end, from C berth to J Berth, is a fully operational area, with D to H berths used mainly for general and break bulk cargoes and J berth for tugs.

The western end of Victoria Quay is a publicly accessible area accommodating port administration functions, a ferry terminal, a market, a new Maritime Museum and other uses. This area is being revitalised as part of the Fremantle Waterfront Development.

Rous Head is a large industrial estate which was created on land reclaimed from material dredged from the Inner Harbour and its shipping access channel. The land is used for a variety of port-related and marine industries.

The Inner Harbour is linked by rail to the interstate and intrastate rail networks.