Plants which grow in the Werribee River catchment play an important role in the life of the river. The herbs, ground covers and grasses all protect the ground from erosion from wind and rain. Grasses, sedges, rushes small bushes and shrubs provide cover and food for a range of insects and animals. Larger shrubs and trees provide wind breaks, food, foliage for habitat and shelter. All plants provide food, shelter and habitat for insects, reptiles, animals and birds.

There are three bioregions in the Werribee River catchment: the Victorian Volcanic Plains; the Central Victorian Uplands; the Otway Plan Bioregion. In the catchment, only approximately a third of native vegetation remains. The region has been extensively cleared due to farming, inappropriate land management practices, and urban development.

However, some outstanding places exist in which flora survives in very good condition. The Wombat Forest, the Brisbane Ranges, and several small protected places such as Truganina Cemetery provide great viewing of wildflowers and unique species. In September 2006, field surveys identified over 75 flora species and nineteen weed species between Mt Cottrell and Bungy’s Hole. The catchment also has several Ecological Vegetation Classes which are considered endangered in the region. This includes Coastal Saltmarsh, Estuarine Wetland, Seagrass Meadow, and Floodplain Riparian Woodland (Melbourne Water, 2015).

The region also has its own species of eucalyptus, which only occurs along the Werribee River and its tributaries. In 2011, the ‘Werribee Blue-Box’ was officially recognised by the National Herbarium of Victoria. Classified as endangered under the Flora and Fauna Guarantee Act (FFG Act), these magnificent trees, grow from 3 to 12 metres. A few ancient specimens have survived in the Werribee Township, but most new growth has come from revegetation planting by Werribee Zoo and Wyndham Council.