The ongoing drought in the Western Cape of South Africa (2014 to present) has called for an urgent need to improve our understanding of water resources in the area. Rivers within the Western Cape are known to surge rapidly after rainfall events. Such storm-flow in natural river catchments in the Jonkershoek mountains has previously been shown to be driven by displaced groundwater, with less than 5% of rainfall appearing in the storm-flow. However, the origin of storm-flow surges within urban rivers in the region remains unknown. In this study, we used stable isotopes in water to illustrate that at least 90% of water in the Liesbeek River during a storm event was rainwater. There was a strong correlation between storm-flow and rainfall rates (P < 0.001, Pearson’s r = 0.86), as well as between the δ18O and δ2H values of river-water and rainwater (δ18O: Pearson’s r = 0.741 (P = 0.001), δ2H: Pearson’s r = 0.775 (P < 0.001)). Storm-flow within this urban river therefore appears to be driven by overland-flow over the hardened urban catchment, rather than piston-flow as seen in natural catchments. Our results support studies suggesting the Liesbeek River could be a target for stormwater harvesting to augment water resources in the city of Cape Town.