With an increasing interest in stormwater harvesting, waterway management authorities are receiving many requests to harvest from urban streams and drains. Many of these requests propose harvesting of low-flows, thus potentially causing further degradation to stream health, and missing out on the opportunity to mitigate impacts of storm flows. We used a gridded rainfall-runoff model to characterize regional low-flow hydrology and use this to develop a low-flow threshold to ensure that stormwater harvesting applications target only storm flows. We found that using the modelled mean daily flow provided a reasonable and easy-to-derive estimate of low-flows. Such estimates can be used to derive catchment-specific passing flow thresholds for stormwater harvesting in urban areas. The approach proposed here ensures that the principles applied to streamflow diversion in rural areas can be readily applied to urban areas. We suggest that more sophisticated estimates of low-flows could be pursued in the future, involving estimates of seasonality.