The Fitzroy estuary is about 13 kilometres long, extending to just north of the Princes Highway at Tyrendarra and possibly also extending up Darlot Creek, a tributary of the estuary and located near Tyrendarra. The estuary is a seasonally closed, salt wedge type estuary within a drowned river valley.

The Fitzroy River is crossed by the Tyrendarra lava flow, just upstream of the Princes Highway at Tyrendarra. This creates a barrier to any further upstream movement of salty water. Although Darlot Creek is a tributary of the Fitzroy estuary, Darlot Creek contributes much higher freshwater inflows to the estuary than the Fitzroy River.

Several plants around the estuary are considered rare or threatened, including the salt paperbark, helmet orchid, bog gum, small sickle greenhood and swamp greenhood.

120 bird species have been identified in the Fitzroy estuary area including 17 species listed under the Flora and Fauna Guarantee Act 1988 and two species listed under the Commonwealth Environment Protection and Biodiversity Conservation Act 1999, including the critically endangered orange bellied parrot.  The estuary is utilised by a number of migratory bird species.

17 species of fish have been recorded including recreational species and Yarra pygmy perch (Nannoperca obscura), which is listed as threatened under the Flora and Fauna Guarantee Act 1988 and as vulnerable under the Environment Protection and Biodiversity Conservation Act 1999. The endangered Spot-tailed quoll (tiger quoll) has also been observed in the area.