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Water quality, along with hydrology, plays an important role in the spatial and temporal dynamics of a range of ecological patterns and processes in large rivers and is also often a key component of river health assessments. Geology and land use are significant drivers of water quality during flow periods while during periods of no-flow, local-scale factors such as evaporation, groundwater influence and the concentration and precipitation of compounds are important. This study explored the water quality changes in two Australian dryland rivers, the Cooper Creek (Lake Eyre Basin) and the Warrego River (Murray-Darling Basin), across different hydrological phases over several years. Water quality varied both spatially and temporally; the greatest spatial variability occurred during the no-flow phase, with temporal changes driven by flow. Concentrations of major anions and cations also varied spatially and temporally, with an overall cation dominance of calcium and magnesium and an anion dominance of bicarbonate. This bicarbonate dominance contrasts with previous data from inland lentic systems where sodium chloride was found to dominate. Such extreme spatial and temporal variability hampers successful derivation of water quality guidelines for these variable rivers and suggests such guidelines would need to be developed with respect to ’flow phase’.