This paper describes the development and testing of a mathematical model as a tool to quantify pathogen loads in Sydney's drinking water catchments. It has been used to identify, quantify and prioritise sources of Cryptosporidium, Giardia and E. coli in the Wingecarribee catchment. The pathogen model promotes understanding of the relative significance of different sources of pathogen risks as well as their fate and transport as they move through the subcatchments. This pathogen model not only enables water utility managers to identify those catchment segments that may contribute the highest load of pathogens, but also where management options will be most effective.