Across Australia sewerage systems are designed with emergency overflow structures to discharge untreated sewage into local waterways in case of system overload or breakdown. Our aim was to determine the impacts of sewage overflows and potential risks to the public and ecosystem health in the tidal waterways of the coastal suburb of Lota. Expectations for improved sewerage system performance are driven by the belief that sewage overflows cause significant environmental harm. However, the research presented here shows that during a large wet weather event, stormwater, and not the overflow, was the dominant stressor of ecological health. Even during dry weather the impacts of overflow events were likely to be low and restricted to the mixing zone at the point of overflow. However, sewage overflows, in dry and wet weather, did pose an unacceptably high public health hazard to potential swimmers in Lota Creek until the overflow stopped and there was a complete tidal exchange with the estuary. This Brisbane City Council/Brisbane Water and Coastal CRC project has provided a sound scientific basis for quantifying overflow impacts and prioritising management of overflows and stormwater. It has also identified the need to develop programs to educate and raise community awareness, assess waterway use and potential pathways that can pose a risk to human health from wet and dry weather overflows both locally and into Moreton Bay.