Determining sources of heavy metals in soils, sediments and groundwater is important for understanding their fate and transport and mitigating human and environmental exposures. Artificially imported fill, natural sediments and groundwater from 240 ha of reclaimed land at Fishermans Bend in Australia, were analysed for heavy metals and other parameters to determine the relative contributions from different possible sources. Fishermans Bend is Australia's largest urban re-development project, however, complicated land-use history, geology, and multiple contamination sources pose challenges to successful re-development. We developed a method for heavy metal source separation in groundwater using statistical categorisation of the data, analysis of soil leaching values and fill/sediment XRF profiling. The method identified two major sources of heavy metals in groundwater: 1. Point sources from local or up-gradient groundwater contaminated by industrial activities and/or legacy landfills; and 2. contaminated fill, where leaching of Cu, Mn, Pb and Zn was observed. Across the precinct, metals were most commonly sourced from a combination of these sources; however, eight locations indicated at least one metal sourced solely from fill leaching, and 23 locations indicated at least one metal sourced solely from impacted groundwater. Concentrations of heavy metals in groundwater ranged from 0.0001 to 0.003 mg/L (Cd), 0.001–0.1 mg/L (Cr), 0.001–0.2 mg/L (Cu), 0.001–0.5 mg/L (Ni), 0.001–0.01 mg/L (Pb), and 0.005–1.2 mg/L (Zn). Our method can determine the likely contribution of different metal sources to groundwater, helping inform more detailed contamination assessments and precinct-wide management and remediation strategies.