A methodology has been developed to apply the materials budget concept, used in sediment and nutrient studies, to construct a pathogen budget for drinking water catchments, taking into consideration pathogen origin, deposition, inactivation and movement within a catchment. These processes can be described in terms of stocks (pathogens) and flows (movement of stocks). In south-eastern Australia, the majority of pathogen loading to major tributaries was predicted to occur during and after high intensity rainfall events where in-stream resuspension was not of great relative importance. In contrast, during dry weather the transit time within the studied catchment was sufficiently long that in-stream processes became relatively important. Total pathogen unit (TPU) budgets were constructed for the parasitic protozoa Cryptosporidium and Giardia. This approach enables water utility managers to identify those catchment segments and processes that are contributing or removing the greatest load of pathogens, and thus where management options will be most effective. With improved knowledge of pathogen ecology this approach can be further refined to provide budgets of infectious pathogen units (IPU), more directed to public health risk endpoints.

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