Northern Gulf remains one of the least studied areas for biodiversity in Australia. However, a combination of local knowledge and sporadic data collection has identified a rich and diverse array of vertebrate fauna. This includes at least 118 mammals, 196 reptiles, 63 amphibian and 455 bird species, including a number of endangered species such as the Golden Shouldered Parrot; Gouldian Finch; Star Finch; Red Goshawk; Northern Quoll and the Yakka Skink.

The region generally supports pre-European vegetation. Over 90% of the landscape is either intact or has been subject to minimal disturbance. Despite the low levels of direct clearing, vegetation communities have been extensively modified by a combination of cattle grazing; exotic pastures; woody weeds; changed fire regimes; pest species, and the more localized impacts of mining and infrastructure development. While landscape connectivity remains high over most of the region, human-induced pressures are significantly impacting the health and composition of regional ecosystems.

Vegetation in the Northern Gulf Region is largely comprised of open woodland dominated by Eucalyptus and Corymbia with a grass understorey, however other common vegetation communities include Paperbark Woodlands, Lancewood on gravelly ridges, bluegrass communities, salt marshes, mudflats, mangroves and sand dunes, small areas of vine thicket, riparian woodlands and the wet tropical rainforests at the headwaters of the Mitchell catchment.

The alarming decline in native mammals that is occurring across the breadth of Northern Australia is also evident in the Northern Gulf Region. Although the precise rate of decline is difficult to establish due to the lack of long term data, recent surveys have verified the absence or very low abundance of small to medium mammals.

The major drivers of biodiversity decline in the region are most likely altered fire regimes, grazing pressure and pests like feral cats and pigs. Whilst some of these pressures have modified the landscape irreversibly, it is still important to enhance areas for their habitat values, particularly in light of climate change impacts, which could stress many wildlife communities to the point of collapse if these habitats become critically degraded.

Areas of high biodiversity value are found in the Einasleigh Uplands, Brooklyn Sanctuary near Mt Carbine, and Blackbraes National Park. Important wildlife refuges also occur within the wetland aggregations along the Gulf Coast, and along riparian corridors throughout the region.

The biodiversity of Gulf Plains Bioregion is the least studied and scientifically understood of the region. There are currently 22 Nature Refuges on private properties throughout the Northern Gulf and a further 23 protected areas, in the form of National Parks and resource reserves, the largest being the Staaten River National Park. The secure tenure of these areas make them ideal candidates for investment toward enhancing habitat values.