Domestic wastewater contains high levels of potentially pathogenic microorganisms. In residential areas not serviced by reticulated municipal sewage networks, domestic wastewater is treated via On-site Sewerage Facilities (OSFs). However, the failure rate of OSFs is reportedly as high as 70%. This may result in contamination of waterways, which can adversely impact stream microbial communities, while also compromising the quality of water received at downstream drinking water treatment plants (WTPs). We developed and applied a spatial analysis method in combination with the Catchment Investment Decision Support System to (1) estimate total daily loads of potentially pathogenic microorganisms arising from OSFs and the level of risk to adjacent streams and water received at a WTP, and (2) to develop an optimised catchment intervention program to reduce loads of potentially pathogenic microorganisms entering waterways in southeast QLD. Results show that over 42,000 OSFs are present across catchments in southeast QLD, with 215 present in our example catchment. In this catchment, 55 OSFs were assessed as posing at high-or very high risk to adjacent stream environments and to water received at the downstream WTP. Daily loads of bacteria and viruses can be reduced from 7.1 log to 6.0 log, and daily loads of protozoa can be reduced from 3.1 log to 2.0 log via upgrade of problematic OSF. Further, our spatial analysis method enables mapping of areas which have the most impact on downstream environments and water quality. This helps facilitate community consultation and ensures that limited budgets for on-ground works are targeted appropriately.