River water quality is driven primarily by discharge and a catchment's natural and anthropogenic features. In this study, the underpinning role of discharge in driving water quality is examined for an Australian tropical savanna river. The seventh-order Daly River has a near-natural discharge regime and catchment that is highly weathered, and has low topographic relief, with most of its natural vegetation retained. Four discharge periods are defined according to surface and groundwater water source, and the magnitude and frequency of run-off events. On a seasonal scale, the river's water quality reflected the mix of water sources. These comprised extremes of high surface water-driven discharge, high suspended sediment concentrations and low water clarity during the wet season, and low groundwater-fed discharge during the dry season with high water clarity. The suspended sediment concentration of run-off events during the dry-to-wet transition and the wet season were directly and inversely related to event maximum discharge respectively, suggesting the exhaustion of sediment supply to the river during the wet season. Variability associated with the discharge-water quality relationships was attributed to water source, hysteresis and event magnitude and timing. Suspended sediment yields and concentrations were relatively low compared with more anthropogenically affected Australian savanna catchments.