Extreme floods, driven by climate change, are becoming more frequent and severe across many regions, but the impacts on water quality are uncertain. The Murray-Darling Basin (MDB), in Australia, is a large arid to semi-arid river system, that has experienced major drought and flood events over recent decades. In this study, we investigated the dynamics of Total Nitrogen (TN), Total Phosphorus, and Dissolved Organic Carbon (DOC) in six major flow events from 2011 to 2023, including a 2022-2023 'mega-flood' the largest since 1956. We applied statistical and hysteresis analysis from 3 study sites, spanning the upper to lower regions in the southern MDB. The mega-flood event accounted for over 30% of the total flow and similar to 18% of the TN and similar to 20% of the TP yield within the entire study period, with higher nutrient peaks and concentrations in downstream sites. This was likely due to a combination of overbank flows, extensive floodplain inundation, and increased nutrient transport from adjacent agricultural catchments. Nutrient concentrations during the mega-flood exhibited distinct counter-clockwise hysteresis, with higher concentrations on the falling limb of the hydrograph, indicating delayed release from floodplains. This contrasts with the upstream headwater site, which showed weak clockwise hysteresis, reflecting rapid hillslope-driven mobilisation. Our findings demonstrate that more frequent climate-driven mega-floods may lead to proportionally larger nutrient loads and prolonged water-quality degradation. However, the magnitude of nutrient export ultimately depends on antecedent catchment conditions and the availability of transport-ready nutrient stores, which can vary substantially between flood events.