The Department of Water Affairs and Forestry (DW AF) is the custodian of South Africa's water resources and its primary role is to maintain the fitness for use of water on a sustained basis. DW AF recognized that management and assessment of fitness for use can only be based on reliable monitoring data. For this purpose DWAF has already for a number of years operated a national programme which collects data on the chemical and physical quality of South Africa's water resources. The microbial quality of surface water is of growing concern in a number of areas in South Africa. Water of poor microbial quality has serious implications for domestic, recreational and agricultural use due to the risk of water-borne diseases. DW AF acknowledged the need for information on the microbial quality of South Africa's water resources to assess and manage the potential health risk to water users. As an initial step the development of a national microbial monitoring programme to assess the faecal pollution of surface waters was initiated. This study describes the development of the conceptual design of such a programme and demonstrates how a novel area prioritization procedure enhanced the design. The focus of the programme was to be areas where human health might be severely impacted by the microbial quality of surface water. To identify such areas, a procedure for the identification and prioritization of specific areas of concern was developed and used as part of the design approach. Two factors were identified for the quantification of the potential health risk. They were the threat of microbial pollution of water (the result ofland use) and the exposure of consumers to the water (sensitivity of water uses). A number of land and water uses information sources therefore served as the basis for determining priority among the different areas. The described approach to identify and prioritize specific areas of concern has a number of benefits. Primarily, the approach assists in focusing the monitoring efforts on problem areas without a need for extensive historical microbial water quality data. The approach could be used to optimize the spatial distribution of sampling stations and assist in determining their national distribution. The approach also allows for phased implementation of the programme which facilitates the development of skills and capacity, as well as required infrastructure needed for the large scale operation of the programme. The approach to focus on impacted areas is generic enough not to be restricted to the design of microbial water quality monitoring systems. Other monitoring objectives could also be dealt with in the same manner. During evaluation of the design on a pilot scale the conceptual design was found to meet the set information objectives. The conceptual design for the programme also deals effectively with constraints and changes in the external environment in which it has to operate. Implementation of the national programme has started and plans to expand the programme are progressing well. The concept of high risk areas and the procedure to identify and prioritize such areas as developed during this study is a critical component of the overall design. The programme appears to address a significant information need on an important aspect of water resources management and to do so in an efficient and effective manner.