[1] The Mary River was used for rafting timber during the early years of European land settlement, and the discovery of gold at Gympie in 1867 brought an inflow of miners and pastoralists.

[14] The high turbidity levels interfered with the natural breeding cycle for some of the river species.

The Mary River flows into the Great Sandy Strait, near wetlands of international significance recognised by the International agreement of the Ramsar Convention and the UNESCO Fraser Island World Heritage Area, which attracts thousands of visitors every year.

[3] The river's catchment area is 9,595 square kilometres (3,705 sq mi) and is bounded by the Conondale, Jimna and Burnett Ranges.

[16] Many parts of the river contain stretches stripped of trees and damaged by hard-hoofed cattle and sand mining.

[16] Counter measures including driving pile fields into the riverbank, tree planting, riparian fencing and the installation of off-stream livestock watering points have stopped thousands of tonnes of sediment from entering the river.

[19] In light of the region's longest drought in one hundred years, the Queensland Government announced on 27 April 2006 its intention to dam part of the Mary River at Traveston Crossing, south of Gympie.

The project was cancelled in November 2009, after being refused approval by Federal Environment Minister Peter Garrett.

[21] There was considerable local opposition to the proposal, with all Mary Valley and Sunshine Coast Shire Councils opposed to the dam proposal[22] on a variety of grounds including: the dislocation of the local community from the inundated area; adverse effects on downstream communities; and environmental impacts such as the removal of one of the few remaining habitats for the vulnerable Queensland lungfish.

[24] There was strong opposition to the dam from the wider and international community, based on environmental concerns related to the endangered Mary River cod, Mary River turtle, giant barred frog, cascade tree frog, Coxen's fig parrot, the vulnerable Queensland lungfish, tusked frog, honey blue-eye fish, the Richmond birdwing butterfly and the Illidge's ant blue butterfly.

It was alleged that reduced fresh water flowing to the Great Sandy Strait would have affected the growth of seagrass, the dugong's primary food source.

Professor Jean Joss of Macquarie University stated, in a submission to the Senate Inquiry 2007: "The Mary River dam would almost certainly push the lungfish to 'Critically Endangered,' and in the long term will lead to its extinction in the wild.