Evaluations of pathogen management options have focussed on assessing relative removal effectiveness as a basis for prioritising alternative management investment decisions. Using a case study of the Myponga catchment, South Australia, this work presents results of a cost-effectiveness risk analysis of catchment- and treatment-based water quality management alternatives for mitigating Cryptosporidium risk. A range of costs and benefits including set-up and operating costs, farm business costs and benefits, and environmental service benefits are considered in comparing the net cost associated with each management alternative. Considering the broader range of costs and benefits changes the relative cost-effectiveness of water quality management alternatives significantly.