Water-borne pathogens such as Cryptosporidium pose a significant human health risk and catchments provide the first critical pollution 'barrier' in mitigating risk in drinking water supply. In this paper we apply an adaptive management framework to mitigating Cryptosporidium risk in source water using a case study of the Myponga catchment in South Australia. Firstly, we evaluated the effectiveness of past water quality management programs in relation to the adoption of practices by landholders using a socio-economic survey of land use and management in the catchment. The impact of past management on the mitigation of Cryptosporidium risk in source water was also evaluated based on analysis of water quality monitoring data. Quantitative risk assessment was used in planning the next round of management in the adaptive cycle. Specifically, a pathogen budget model was used to identify the major remaining sources of Cryptosporidium in the catchment and estimate the mitigation impact of 30 alternative catchment management scenarios. Survey results show that earlier programs have resulted in the comprehensive adoption of best management practices by dairy farmers including exclusion of stock from watercourses and effluent management from 2000 to 2007. Whilst median Cryptosporidium concentrations in source water have decreased since 2004 they remain above target levels and put pressure on other barriers to mitigate risk, particularly the treatment plant. Non-dairy calves were identified as the major remaining source of Cryptosporidium in the Myponga catchment. The restriction of watercourse access of non-dairy calves could achieve a further reduction in Cryptosporidium export to the Myponga reservoir of around 90% from current levels. The adaptive management framework applied in this study was useful in guiding learning from past management, and in analysing, planning and refocussing the next round of catchment management strategies to achieve water quality targets.