Although there has been a loss of native freshwater fish species in the system, the Werribee River catchment still provides an important habitat for native fish. The upper reaches are home to the River Blackfish, Trout Galaxias and Mountain Galaxias, while the lower reaches in and around Werribee, are home to Australian Smelt, Common Galaxias, Congoli, Flathead Gudgeon, Pouch Lamprey, Shorthead Lamprey. Estuarine and lower freshwater reaches support a healthy recreational fishery, including Estuary Perch, Black Bream and King George Whiting.
Introduced fish species are found throughout the catchment, with Redfin, Roach, Tench, Goldfish and European Carp becoming more common downstream. Impacts of introduced species include predation on native fish and competition for food and habitat.
There are 11 frog species in the Werribee River catchment, two of which are threatened, the Growling Grass Frog and Bibron’s Toadlet. Conserving and appropriately managing habitats in the region is vital for the survival of each frog species. Some are adapted to riverine environments, while others are wetland or slow-flowing river species. Ensuring a varied and healthy habitat is important to ensure the survival of the species that are present in the catchment.
Other key species in the catchment include the Growling Grass Frog, Striped Legless Lizard and Golden Sun Moth.
Platypus are distributed throughout the Werribee River catchment where there are reliable summer flow regimes. However, they are considered locally threatened due to low numbers. The WRivA began the first surveys of platypus in the Werribee River in 1997-1998. With the help of a City of Wyndham grant, WRivA engaged Platypus Conservancy Australia to carry out a series of platypus net surveys in the lower Werribee River, below the Werribee Diversion Weir. The survey captured 16 individual animals over three nights in that summer. It was concluded that the density of the animals was three individuals to the kilometre. The surveys were repeated in 1999-2000 but with a smaller number of eight individual recorded, half of which had evidence of cuts and scars due to encounters with fishing line or litter. Surveys were undertaken again in 2010, but numbers were down again, as was common in other waterways across Melbourne, possibly due to low water levels following the years of the Millennium drought.
Since 2015, WRivA has been engaged in environmental DNA research with Melbourne Water in the lower Werribee River. Laboratory results of the water samples taken to be analysed have been positive on most occasions for the presence of platypus. In 2018, seven platypuses were killed out of a local population of less than 50 when caught in an illegal fishing net.