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Nitrate contamination of groundwater is an environmental concern in intensively cultivated desert oases where this polluted groundwater is in turn used as a major irrigation water resource. However, nitrate fluxes from root zone to groundwater are difficult to monitor in this complex system. The objectives of this study were to validate and apply the WHCNS (soil Water Heat Carbon Nitrogen Simulator) model to simulate water drainage and nitrate leaching under different irrigation and nitrogen (N) management practices, and to assess the utilization of groundwater nitrate as an approach to remediate nitrate contaminated groundwater while maintain crop yield. A two-year field experiment was conducted in a corn field irrigated with high nitrate groundwater (20 mg N L-1) in Alxa, Inner Mongolia, China. The experiment consisted of two irrigation treatments (I-std, standard, 750 mm per season; I-csv, conservation, 570 mm per season) factorially combined with two N fertilization treatments (N-std, standard, 138 kg ha(-1); N-csv, conservation, 92 kg ha(-1)). The validated results showed that the WHCNS model simulated values of crop dry matter, yield, soil water content and soil N concentration in soil profile all agreed well with the observed values. Compared to the standard water management (I-std), the simulated drainage and nitrate leaching decreased about 65% and 59%, respectively, under the conservation water management (I-csv) Nearly 55% of input N was lost by leaching under the IstaNstd and IstdNav treatments, compared to only 26% under the IcsvNstd and IcsvNcsv treatments. Simulations with more than 240 scenarios combing different levels of irrigation and fertilization indicated that irrigation was the main reason leading to the high risk of nitrate leaching, and the nitrate in irrigation groundwater can be best utilized without corn yield loss when the total irrigation was reduced from the current 750 mm to 491 mm. This reduced irrigation rate facilitated the use of approximately 42 kg N ha(-1) yr(-1) of nitrate from groundwater, which would gradually improve the groundwater quality. Future field studies on nitrate leaching in this area are suggested to investigate water and N dynamics under irrigation rates near 490 mm per season. (C) 2016 Elsevier Ltd. All rights reserved.