The headwaters of the river rise on the coastal plain of the Cape York Peninsula and flow in a north westerly direction eventually discharging at Evans Landing into Albatross Bay near Nanum just south of Weipa and into the Gulf of Carpentaria.

The river has a catchment area of 4,622 square kilometres (1,785 sq mi) of which an area of 392 square kilometres (151 sq mi) is composed of estuarine wetlands.

[3] From source to mouth, the Embley River is joined by five tributaries including the Hey River.

The Embley River descends 21 metres (69 ft) over its 54-kilometre (34 mi) course.

[2] The river was named in 1895 by John Douglas CBE after the surveyor, John Thomas Embley (1858-1937), while Douglas was Government Resident on Thursday Island.