[2] The Crocodile River has its source in the Witwatersrand ridge, originating in Constantia Kloof, Roodepoort, Gauteng province.

The effects of pollution from two of South Africa's metropolitan areas, Johannesburg and Tshwane, has been detrimental to the ecology of the system.

Untreated industrial, mining, agricultural and household waste has deteriorated the water quality throughout most of its course and led to massive algal blooms in the Hartbeespoort Dam and Roodekoppies Dam.

Invasive plant species have negatively affected the integrity of the system.

Unsustainable farming practices have led to sediment overloads and erosion further harming the river.