The river rises on the northern slopes of Boulder Mountain at Valley of Lagoons, part of the western slope of the Seaview Range, and flows into the Coral Sea at Upstart Bay over 200 kilometres (124 mi) to the southeast of the source, with a catchment area of approximately 130,000 square kilometres (50,000 sq mi).

The source of the Belyando River in central western Queensland is almost 500 kilometres (311 mi) from the mouth of the Burdekin River, and extends into the typical black-soil grassland of Central Queensland, with the Belyando draining the Drummond and Galilee Basins and flowing north for over 1,000 kilometres (620 mi).

The first is at the Valley of Lagoons in the upper region of the catchment, the next is a Lake Dalrymple,[11] then at the junction of the Burdekin and Bowen rivers known as the Burdekin-Bowen Junction and Blue Valley Weir Aggregation[12] and the last is at the river delta which forms a 342.5 square kilometres (132 sq mi) wetland.

Annual rainfall at most gauges within the basin can range from 200 to 1,600 millimetres (7.9 to 63.0 in) depending on the monsoon and the number of cyclones that cross the coast.

Both were too low and often damaged during flooding and the decision was made to replace them with a higher dual level bridge known as the Silver Link.

[4] A weir was constructed in a gorge in the Leichhardt Range for settlement farms near Clare and Dalbeg in 1953 for growing tobacco.

[17] Heavy flooding occurred in 1875 with the Dawson, Fitzroy, Mary and Burdekin Rivers rising up to 60 feet (18 m) in a few hours.

[26] During the 1974 flood event associated with Cyclone Wanda, which lasted from 17 December 1973 to 23 April 1974, an estimated mass discharge peak of 25,000 tonnes (25,000 long tons; 28,000 short tons) of water per second was reached, which affected 450 kilometres (280 mi) of coastline and created a plume with widths ranging from 25 to 100 kilometres (16 to 62 mi).

[29] Major pump stations are located at Clare Weir feeding water to both sides of the river.

The use of groundwater in the floodplain is carefully managed so that supply can be maintained during the dry season and to prevent saltwater intrusion.

[30] The North Coast railway line crosses the river at Home Hill, via a bridge constructed in 1913.

The area was plagued by cattle tick, so the government acquired the property in 1910 and sold it off as farmland where sugarcane was later grown.

Near the coast there are patches of dry eucalypt forest on the typically infertile laterised soils characteristic of most of Australia.

[34] Many other species such as Agassiz's glassfish, Irwin's turtle, banded grunter, barramundi, black catfish, eastern rainbowfish, empire gudgeon, freshwater longtom, mangrove jack, tilapia and yellowbelly are found throughout the catchment.