The river rises from the eastern slopes of the Blackall Range and flows east through Eumundi before entering the sea at Cotton Tree, Maroochydore.

The watershed of the Maroochy River encompasses 630 square kilometres (240 sq mi) of undulating hills, which have been cleared for agriculture and urban uses.

[6] The Maroochy River is part of a blue carbon initiative, Australia's first partnership, that undertakes to provide land use options for recreation, farming and the like via environmentally effective approaches that maintain and improve the natural environment.

[11] By 1930, the growth of urban settlements improved due to changes in transport access in the Maroochy River region.

[11] The mouth of the river was affected by the 2009 southeast Queensland oil spill, reaching about 2 kilometres (1.2 mi) upstream of the Maroochy Bridge.