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Groundwater recharge and discharge in the Akesu alluvial plain were estimated using a water balance method. The Akesu alluvial plain (4842 km(2)) is an oasis located in the hyperarid Tarim River basin of central Asia. The land along the Akesu River has a long history of agricultural development and the irrigation area is highly dependent on water withdrawals from the river. We present a water balance methodology to describe (a) surface water and groundwater interaction and (b) groundwater interaction between irrigated and non-irrigated areas. Groundwater is recharged from the irrigation system and discharged in the non-irrigated area. Uncultivated vegetation and wetlands are supplied from groundwater in the hyperarid environment. Results show that about 90% of groundwater recharge came from canal loss and field infiltration. The groundwater flow from irrigated to non-irrigated areas was about 70% of non-irrigated area recharge and acted as subsurface drainage for the irrigation area. This desalinated the irrigation area and supplied water to the non-irrigated area. Salt moved to the non-irrigation area following subsurface drainage. We conclude that the flooding of the Akesu River is a supplemental groundwater replenishment mechanism: the river desalinates the alluvial plain by recharging fresh water in summer and draining saline regeneration water in winter. Copyright (C) 2007 John Wiley & Sons, Ltd.