Wet weather sewer overflows pose potential short-term public health risks. With increasing populations, aging infrastructure and climate change, utilities are challenged with managing sewerage infrastructure to provide optimum outcomes. This study compared how modelled public health risk profiles could change under alternative sewer overflow management strategies during 12 and 24-month rainfall-runoff events. Specifically, existing conditions were compared with both a ‘business-as-usual’ (BAU) sewer upgrade and a more holistic ‘effects-based planning' (EBP) approach based on pumped wet weather sewage overflows directed to a local receiving waterway. Options were compared based on their efficacy to reduce manhole overflows, recreational waterway guideline exceedances and downstream recreational waterway health risks estimated through a screening-level Quantitative Microbial Risk Assessment (QMRA). Results indicated that the two management strategies would be equally effective in reducing the frequency, duration and volume of manhole sewer overflows, eliminating them in the 12-month scenarios and reducing them from >5000 m3 for the 24-month baseline scenario, to 23 and 35 m3 for BAU and EBP, respectively. Baseline, BAU and EBP scenarios produced similar hours of enterococci guideline exceedances, ranging from 1 to 4 h difference. The QMRA produced similar health risk profiles for downstream recreational waterway users for all design events, suggesting that sewer overflows are not the primary driver of public health risks during and immediately following high rainfall events. As such, QMRA provided evidence that an EBP strategy may be used to manage wet weather sewer overflows in lieu of an expensive BAU upgrade, without exacerbating the public health of downstream waterway users. Further investigation of the broader environmental health impacts of implementing this type of innovative approach is warranted. Nonetheless, this work highlights the value of integrating QMRA with other modelling approaches to guide and inform sewer overflow management.