The 122.7 km long river has a drainage basin of 2,636 km2[1] and flows in a roughly north–south direction, originating from Mount Gemuruh and then empties into the Strait of Johor.

The river and tributaries are important sources of water supply not only for the state itself but also for neighbouring Singapore.

In addition, the Linggui Dam completed and impounded in 1993 also supplements the water supply to both Johor and Singapore.

Evidence of the presence of a viable breeding population of dugongs in the waters of the Johor River estuary was collected between 1974 and 1989.

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