Input-Output Assessment (IOA) was employed to quantify a likely range of annual lead and cadmium fluxes and to discern their possible flow paths in the water system of the Kingston hydrological catchment in south-eastern Jamaica. This technique was useful to understand how cross-sectoral mass exchanges of these heavy metals ultimately impacted the water resources of the basin. Initially, based on deterministic principles of the urban hydrological cycle, a foundational IOA matrix model was formulated to represent the basin’s typical annual hydrological regime. Here, flows of the water-using or water-impacting sectors that comprise the basin’s water system were identified and quantified. Hereafter the realistically possible cases of minimum, average and maximum direct cross-sectoral mass flows of lead and cadmium were estimated. The heavy metal mass flows of each case were calculated by multiplying the various annual cross-sectoral water flux volumes by corresponding lead and cadmium concentrations. The resulting direct flow matrices  were then stochastically recalculated to succinctly represent the most statistically likely coupled direct and indirect lead and cadmium mass flows in models. After the flux modelling was completed, backward and forward tracing of the mass fluxes identified natural water resources as recipient of most lead and cadmium in the basin. This is arguably the most noteworthy finding of the study as the natural water bodies were loaded even when the water system was modelled to show the minimum likely mass flows of lead and cadmium. From the average and maximum likely fluxes of lead and cadmium, not only did the loading of the natural water resources increase but they in turn started to distribute lead and cadmium to other water bodies. Tracing also identified anthropogenic activities as the driver of lead and cadmium cycling throughout the system. The study was concluded in the recommendation of a strategy to improve wastewater treatment facilities and coverage as the most efficient and cost effective way to ameliorate the degree of lead and cadmium cycling and loading in the water resources of the basin.