The Mary River Cod is listed as Endangered under the Environment Protection and Biodiversity Conservation Act 1999 and is estimated to only occur in less than 30% of its historic range.

This overfishing, combined with the massive siltation of their habitats by land clearing, destruction of riparian vegetation and cattle trampling river banks, and dams and weirs blocking migration, rapidly caught up with this large, slow-growing, long-lived Maccullochella cod species, as it has with all its close relatives.

[5] Outside of a few stocked Queensland impoundments- upstream of the walls of Cressbrook, Hinze, Maroon, Moogerah, North Pine, Somerset, and Wivenhoe Dams and lakes Dyer (Bill Gunn dam) and Clarendon- the fish is a no-take species, and any caught should be carefully released.

[3] A strict bag limit of one fish with a minimum size of 50 cm applies to the stocked impoundments.

As of 2010, after studies of mitochondrial and nuclear DNA, the Mary River cod has been raised to full species status.