Management decisions regarding the potential fate and toxicity of anthropogenic metal elements requires a knowledge of metal partitioning and speciation as mediated by in situ control systems (ICS). This study focussed on Cd, Zn, Cu and Pb, common anthropogenic metal elements generated in the built environment and examined the influence of variable event-based hydrology and passive ICS by an engineered partial exfiltration reactor (PER) system on partitioning and speciation. The feasibility and efficiency of the PER as an in situ stormwater runoff control strategy to attenuate levels of metal elements was evaluated. Results indicate that higher rainfall intensity resulted in higher dissolved fraction (fd) values for influent Zn, Cu and Cd, but did not have a significant influence on partitioning of Pb. Speciation indicated that divalent fractions of Cd, Zn, Cu and Pb were changed marginally by the PER. Cu and Pb mainly complexed with organic matter in the influent, while carbonate complexes of these metals in the effluent significantly increased. The PER consistently and statistically reduced all loadings of Cd, Cu, Pb and Zn for all examined events, whether on a mass or concentration basis. As an unsaturated flow unit operation/process the PER can efficiently remove ionic or complexed forms of metal elements. Such UOPs are a potential quality and quantity ICS strategy for rainfall-runoff.