[4] The park contains almost 500 species of native plants, 23 of which are classified as threatened, including the Northern Sandalwood (Santalum lanceolatum) and the Narrow Goodenia (Goodenia macbarronii), both of which have action statements under the Flora and Fauna Guarantee Act 1988 (Vic), and the Spur-wing Wattle (Acacia triptera), which only occurs in Victoria in the Warby ranges.

[5] The Santalum lanceolatum (Northern Sandalwood), which is a small tree or tall shrub and has highly aromatic wood, dark, furrowed bark and thick, grey-green leaves, was historically widespread and common to the rocky faces of the Warby ranges.

It has basal leaves which are narrow-obovate to linear oblanceolate, thick with coarse teeth around the edge and may have several rosettes linked by short underground stems.

[7] The Grass Tree (Xanthorrhoea glauca subspecies angustifolia), which was listed under the Flora and Fauna Guarantee Act 1988 (Vic) as endangered in 2013, occurs in low fertility soils primarily in the Box-Ironbark forest area of the park.

Mature grass trees have been found to be sensitive to fire, with high mortality rates occurring after controlled fuel reduction burns.

[12] During the summer months when the Inland Carpet Python is most active, they seek out more open habitat in search of their prey, which consists of small to medium-sized mammals, with European rabbits (Oryctolagus cuniculus) making up 50-80% of their diet.

[4] The Squirrel Glider (Petaurus norfolcensis) is a nocturnal, arboreal mammal found from Queensland through New South Wales to Victoria and is listed as endangered in the southern part of its range, which includes the Warby-Ovens National Park.

Squirrel gliders also feed on arboreal insects, including beetles and caterpillars, and acacia gum, eucalypt pollen, nectar and sap.

[4] The Grey-crowned Babbler (Pomatostomus temporalis) occurs in the Box-ironbark forests in the north of the park and is classified as endangered in Victoria, and has an Action Statement under the Flora and Fauna Guarantee Act 1988 (Vic).

[19][20] They are classified as endangered in Victoria as they are the only member of their genus, Xanthomyza,[4] and their previously wide distribution ranging from north of Brisbane to Adelaide has contracted as forest has been cleared for agriculture.

[20][21] The Regent Honeyeater breeds between September and February, with nests located between 4 and 25 meters above ground level in forks in trees, and constructed from strips of bark, dried grass and other plant materials.

[23] The Powerful owl pairs for life and nests in hollow trees during winter, with the young remaining dependent on the adults until they are eight months old.

[25] Environmental threats to the flora and fauna of the Warby-Ovens National Park include fire, pests and invasive species, habitat fragmentation and disease.

The Warby-Ovens National Park has a number of roads running through it which fragments the habitat of species including the Squirrel glider (P. norfolcensis), which relies on trees being close enough together to be able to glide between them.

[13] Road and access tracks can aid in the spread of the soil-borne plant disease Phytophthora cinnamomi, which affects several species within the park, including the Daphne Heath and Grass Trees.

[25] Pests and invasive species are key threats to the parks flora and fauna, with the Inland Carpet Python (Morelia spilota metcalfei) being susceptible to predation by wild dogs and foxes.

[21][26] Pest plant species such as Patersons curse (Echium plantagineum), St. Johns Wort (Hypericum perforatum), Quaking grass (Briza sp.)

[4][13][23] Areas of the park that contain species sensitive to fire are protected from fires and prescribed fuel reduction burns by assigning Special Protection Areas - Natural Values, which contain the Northern Sandalwood (Santalum lanceolatum), the Spur-winged wattle (Acacia triptera) and grass trees (Xanthorrhoea glauca angustifolia).

[4] Parks Victoria is working with adjacent landholders to build partnerships to aid in the protection of remnant vegetation on private land, and to undertake pest animal and plant control programs.