Rapid urbanisation and industrialisation have placed increased pressure on the ecosystem health of urban estuaries. Sustainable drainage systems (SuDS) are globally accepted practices for managing the water quality of stormwater and effluent discharged into urban systems. The Swartkops Estuary in South Africa is a heavily urbanized estuary that has a long history of pollution, specifically trace metal contamination, originating from industrial sources and urban wastewater. Using a novel SuDS treatment train, the physical characteristics (total suspended solids), macronutrients (orthophosphates, nitrate, ammonium), trace metals (As, Cd, Hg, Fe, Pb, Cu), and E. coli concentrations were measured monthly for one year, both before and after the treatment train. The treatment train consisted of five interconnected 500 L plastic tanks for sedimentation, filtration (sand and stone), biodegradation and floating wetlands. Results indicate that the SuDS treatment train provided an efficient method in reducing the pollution load to this urban estuary, by reducing macronutrient concentrations by 76 %, trace elements concentrations by 74 % and faecal bacteria counts (E. coli) by 80 %.