Purpose The objective of the current research was to provide a strategy to remediate stormwater from an old, highdeveloped catchment dominated (94%) by diffuse sources. Contaminated catchment soils, a dense road network and extensive residential development have resulted in degraded sediments in the receiving basin. Retrofitting stormwater remedial devices in such catchment-estuarine systems is difficult, costly and long term. Materials and methods The metal content of soils, road dust and gully pot deposits was investigated to assess catchment sources. Fluvial input was assessed using loading models and analyses of water and bedload sediments in two canals draining the catchment, whereas 45 surficial samples were collected from the adjacent estuary to determine impact. All materials were digested using aqua regia and analysis was by inductively coupled plasma (ICP) mass spectrometer and ICP plasma atomic emission spectrometer. Sediment quality guidelines were used to make an initial assessment of degradation by single chemicals and the mean ERM quotient approach was used to determined probable toxicity for mixtures of contaminants. An additional 13 samples were subjected to four laboratory ecotoxicological tests. Results and discussion Soil (mean 62, 410 and 340 μg g −1 for Cu, Pb and Zn, respectively) and sediments (mean 180, 320 and 640 μg g −1 , respectively) in the catchment-estuary system (Iron Cove, Sydney Harbour, Australia) contain greatly elevated metal concentrations. Contaminants associated with baseflow (none, or <5 mm day −1 rainfall) are deposited close to the mouths of two canals discharging to the estuary and this sediment is toxic to benthic animals, whereas chemicals carried by high flow (>50 mm day −1 rainfall) bypass the cove in a buoyant, freshwater plume. Remediation of baseflow and some first-flush stormwater will remove approximately 10% metals and 30-50% TN trapped in the embayment and harvest 2 to 4 ML day −1 of urban water runoff. Conclusions The current approach provides an opportunity to remove a large proportion of total stormwater-derived metals and TN trapped in the adjacent embayment, inexpensively and rapidly. The scheme will prevent stormwater-related chemicals from being deposited in the waterway where adverse biological risk is highest. The potential for recycling and harvesting enormous volumes of treated stormwater in highly desirable parts of intensely urbanised environments is in keeping with the concept of "cities as water supply catchments".