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The headwaters of the river rise south east of Glenden, Queensland and flow in a generally southern direction, crossing the Peak Downs Highway near Moranbah. It continues past Iffley and veers eastward at Leichhardt Downs forming a series of braided channels, and veers south east again and flows past the eastern edge of Junee State Forest and then discharges into the MacKenzie River of which it is a tributary.
The river has a catchment area of 22,364 square kilometres (8,635 sq mi) of which an area of 474 square kilometres (183 sq mi) is composed of riverine wetlands.
The river was named for the pastoralist Frederick Nevil Isaac by the explorer Ludwig Leichhardt who came across the river during his 1845 expedition through the area to Port Essington (now Darwin). Isaac owned Gowrie Station on the Darling Downs and was a keen supporter of Leichhardt.