The river flows through the Werribee Gorge State Park before being utilised for irrigation of market gardens at Bacchus Marsh, then through Werribee before flowing through the Werribee Open Range Zoo in Werribee Park, and finally the small coastal settlement of Werribee South before entering Port Phillip bay. The Western Water Treatment plant, a sewage treatment site, is located near the mouth of the river, and supplies irrigation needs to the Open range zoo.
The Werribee River Trail winds beside the Werribee River from Presidents Park, Wyndham Vale to the Princes Highway in Werribee.
The explorers Hume and Hovell camped by the river on 15 December, 1824 and named it the Arndell after Hovell's father-in-law. John Helder Wedge 're-discovered' the river in 1835 and initially called it the Peel, but then decided to call it the Ex or Exe. Exford, an early crossing place on the river, is derived from this name. One of the local Wautharong speaking Kulin tribesman that accompanied Wedge said the name for the stream was 'Weariby Yallock' ('yallock' meaning 'stream'). The spelling changed to the present form of Werribee, and the original aboriginal word meant spine or backbone.
In the late 1830s and 1840s the Werribee River was the scene of conflicts between the Wautharong people and the European colonisers. The squatter Charles Franks and a shepherd were speared to death near Mount Cottrell in July 1836. This resulted in a punitive party led by John Batman which came upon a large party of aborigines and indiscriminately shot and killed at least ten. There are accounts of arsenic laced flour being given to local aborigines.
In 1851 a substantial timber bridge was built to cross the Werribee River to replace an earlier wooden bridge. In 1852 this bridge was washed away when the Werribee river flooded.
In August 2004 the Victorian Government pledged $300,000 towards restoring the Werribee River, removing willows choking the river around the township and replacing them with native plants in a habitat restoration project.