This article examines the storage, transfer and cycling of metals within water, soil and sediment systems in and around Mount Isa Queensland, Australia. The impacts and risks arising from agricultural activities, Mount Isa mine ore extraction, sewage treatment releases, urban runoff on the downstream Leichhardt River and associated drinking water supplies are considered. The ephemeral Leichhardt River bisects the City and the Mine and drains downstream to Lake Moondarra where the City’s water is captured and stored. During the dry season the channel is characterised by numerous pools that act as storage zones for sediment and water-soluble metals as well as urban and agriculturally derived and pathogens. Our results show that sediment and water quality within the Leichhardt River adjacent to and downstream of the mine frequently exceed Australian government sediment guidelines with average values of Cu-1550; Pb-510 and Zn-470 ppm found adjacent to the footprint of the mine. Dry season analysis of water-soluble Cu, Pb and Zn concentrations within pools showed that Australian government low trigger guidelines are exceeded in 100; 56 and 100 % of cases, respectively. The pathogen content of water stored in remnant pools also exceeded acceptable guidelines with maximum faecal coliform densities of 220 CFU/100mL and Enterococcus values of 900 orgs/100mL. The impacts on biota were also examined by assessing the metal content of the flesh of seven fish (three species) and three crayfish from Lake Moondarra for their Cd-Cu-Hg-Pb-Se-Zn concentration. Flesh metal values were generally low but mean Zn concentrations exceeded the guideline value for each of the species. In the three crayfish samples, the mean Cu concentration exceeded the guideline value marginally. The effectiveness of the City’s natural reed-bed potable water processing facility for removing metals held with the water body (soluble and particulate) was also assessed. The results show that the treated water generally meets Australian drinking water guidelines. Overall it is clear that sediment and water quality in the area upstream of the potable water storage zone is seriously impaired. The combined effects of industrial, agricultural and urban activities present a considerable risk to the consistency and reliability of water quality, especially during highly turbid wet season flows that are shown to transfer highly elevated water-soluble metal concentrations.