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Lateral exchanges of surface water between river channels and their floodplains are important for vegetation health and aquatic food-web productivity in semi-arid ecosystems. However, the significance of the lateral connectivity via sub-surface pathways in these systems is not as well understood. Patterns in nitrogen concentration in groundwater and in the unsaturated zone were used to infer the sub-surface biogeochemistry of N in the riparian zone of a large semi-arid floodplain (Hattah-Kulkyne National Park) of the River Murray, Australia. The riparian zone plays a special role in this system as it is an area of transition between fresh surface waters and saline floodplain groundwater. The river was losing water to the floodplain during baseflow conditions but gradients were temporarily reversed following floods. In general, the redox conditions were sub-oxic to anoxic in riparian groundwater and the main forms of N present were NH(4)(+) and dissolved organic N. There was a gradient in NH(4)(+) concentration from the river to the floodplain, suggesting that the main source of NH(4)(+) was from the decomposition of organic matter in fluvial sediments. Elevated concentrations of NO(3)(-) were occasionally found in shallow groundwater away from the fiver following floods but tended not to persist. The source of the NOT appeared to be unsaturated-zone NO(3)(-) displaced to the water table during floods. Assuming that denitrification was the main attenuation process, this displacement of unsaturated zone NO(3) to anoxic groundwater could be a significant N removal process from the ecosystem (estimated at 18 kg N ha(-1) for the largest flood during the study). Understanding the impact of river regulation on floodplain nutrient cycles in River Murray floodplains will be challenging because the changes in floodplain hydrology are complex and coincide with salinization of soils and groundwater. Copyright (c) 2005 John Wiley & Sons, Ltd.