The development of a waste discharge charge system (WDCS) in South Africa has been proposed to promote waste reduction and water conservation. The WDCS is based on the polluter pays principle and is designed such that the management of waste discharges achieves resource quality objectives (RQOs) at the minimum total cost to the catchment. Two charges are distinguished: first a charge for optimising use of the resource (incentive charge); and secondly, a charge for development and operation of mitigation measures in the resource (mitigation charge). The WDCS is applied to both point sources and non-point sources (NPS) of contamination. In the inclusion of NPS, the charge system distinguishes between registered and non-registered NPS, with the charge applied to the former group only, in the first instance. This paper introduces the WDCS by describing the principles and the theoretical basis of the WDCS, highlighting the link to RQOs as the benchmark of acceptable externalities. The paper explores the inclusion of NPS in the WDCS, describing: first, the principles of NPS inclusion in the WDCS; secondly, the types of NPS included in the present version of the WDCS; thirdly, the methodology for charge estimation; and finally, non-registered NPS and their potential inclusion in future editions of the WDCS. The paper concludes with remarks and challenges facing the first edition of the WDCS.