Abstract The Crocodile River is situated in the north east of the Republic of South Africa. It is a large river basin with a total length of 320 km and draining a catchment of 10,450 km2. The water quality of this river is of high importance in sustaining the people and businesses relying on the sustainability of the river. The aim of the study was to use fish and water quality data to determine the present ecological state of the river and identifying the possible sources of pollution in the river.