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This study describes the spatial and temporal variability of water salinity of the Neales-Peake, an ephemeral river system in the arid Lake Eyre basin of central Australia. Saline to hypersaline waterholes occur in the lower reaches of the Neales-Peake catchment and lie downstream of subcatchments containing artesian mound springs. Flood pulses are fresh in the upper reaches of the rivers (< 200 mg 1(-1)). In the salt-affected reaches, flood pulses become increasingly saline during their recession. It is hypothesized that leakage from the Great Artesian Basin deposits salt at the surface. This salt is then transported by infrequent runoff events into the main river system over long periods of time. The bank/floodplain store downstream of salt-affected catchments contains high salt concentrations, and this salt is mobilized during the flow recession when bank/floodplain storage discharges into the channel. The salinity of the recession increases as the percentage of flow derived from this storage increases. A simple conceptual model was developed for investigating the salt movement processes during flow events. The model structure for transport of water and salt in the Neales-Peake catchment generated similar spatial and temporal patterns of salt distribution in the floodplain/bank storage and water flow as observed during flow events in 2000-02. However, more field-data collection and modelling are required for improved calibration and description of salt transport and storage processes, particularly with regard to the number of stores required to represent the salt distribution in the upper zone of the soil profile. Copyright (c) 2005 John Wiley & Sons, Ltd.