This article discusses the location, type and sources of water contamination within the upper reaches of the ephemeral Leichhardt River, NW Queensland. The study specifically examines water quality in a series of the disconnected dry season remnant pools, which occur 19 km upstream of Lake Moondarra, Mount Isa’s potable water reservoir. These pools are significant because they provide a vital drinking water source for native and domestic fauna, but more importantly, are often used for recreational swimming and as an important aboriginal meeting place. The city’s sewerage infrastructure, associated wastewater reuse scheme and Cu and Pb-Zn-Ag mining and smelting activities have been identified as contributors to impaired water quality within the catchment. Five of the fourteen sites tested were found to be unfit for primary human contact as a result of faecal contamination. All sites exceeded the aquatic guidelines for healthy ecosystems (ANZECC, 2000) for TP and TN. Water soluble Cd, Cu, Pb and Zn concentrations exceeded the ANZECC (2000) lower limit for ecosystem survival in five of the nine pools examined. In addition, eight pools exceeded the upper ANZECC guideline (2000) values for soluble Cu.