Deciphering the connection between streamflows and nitrate (NO3-) discharge requires identification of the various water flow pathways within a catchment, and the different time-scales at which hydrological and biogeochemical processes occur. Despite the complexity of the processes involved, many catchments around the world present a characteristic flushing response of NO3- export. Yet the controls on the flushing response, and how they vary across space and time, are still not clearly understood. In this paper, the 'flushing response' of NO3- export from a rural catchment in Western Australia was investigated using isotopic (deuterium), chemical (chloride, NO3-) and hydrometric data across different antecedent conditions and time-scales. The catchment streamflow was at all time-scales dominated by a pre-event water source, and the NO3- discharge was correlated with the magnitude of areas contributing to saturation overland flow. The NO3- discharge also appeared related to the shallow groundwater dynamics. Thus, the antecedent moisture condition of the catchment at seasonal and interannual time-scales had a major impact on the NO3- flushing response. In particular, the dynamics of the shallow ephemeral perched aquifer drove a shift from hydrological controls on NO3- discharge during the 'early flushing' stage to an apparent biogeochemical control on NO3- discharge during the 'steady decline' stage of the flushing response. This temporally variable control hypothesis provides a new and alternative description of the mechanisms behind the commonly seen flushing response. Copyright (c) 2006 John Wiley & Sons, Ltd.