A chemical pollution assessment and prioritisation model was developed for the Upper and Middle Vaal water management areas of South Africa in order to provide a simple and practical Pollution Index to assist with mitigation and rehabilitation activities. Historical data for 2003 to 2008 from 21 river sites were cubic-interpolated to daily values. Nine parameters were considered for this purpose, that is, ammonium, chloride, electrical conductivity, dissolved oxygen, pH, fluoride, nitrate, phosphate and sulphate. Parameter selection was based on sub-catchment pollution characteristics and availability of a consistent data range, against a harmonised guideline which provided five classes. Classes 1, 2, 3 and 4 used ideal catchment background values for Vaal Dam, Vaal Barrage, Blesbokspruit/Suikerbosrant and Klip Rivers, respectively. Class 5 represented values which fell above those for Klip River. The Pollution Index, as provided by the model, identified pollution prioritisation monitoring points on Rietspruit-W:K2, Natalspruit:K12, Blesbokspruit:B1, Rietspruit-L:R1/R2, Taaibosspruit:T1 and Leeuspruit:L1. Pre-classification indicated that pollution sources were domestic, industrial and mine effluent. It was concluded that rehabilitation and mitigation measures should prioritise points with high classes. Ability of the model to perform simple scenario building and analysis was considered to be an effective tool for acid mine drainage pollution assessment.