© 2015 Elsevier B.V.. Groundwater is an important factor that needs to be considered when evaluating the water balance of the soil-plant-atmosphere system and the sustainable development of arid oases. However, the impact of shallow groundwater on the root zone water balance and cotton growth is not fully understood. In this study, we have first analyzed the influence of the groundwater table depth on the seasonal maximum leaf area index of cotton, the average seasonal water stress, cotton yield, actual transpiration, actual evaporation, and capillary rise using experimental data collected at the Aksu water balance station, in Xinjiang, northwest of China and the Hydrus-1D variably-saturated soil water flow model coupled with a simplified crop growth model from SWAT. The coupled model has been first calibrated and validated using field observations of soil water content, leaf area index, cotton height, the above ground biomass, and cotton yield comparisons between measured and modeled variables have shown a reasonable agreement for all variables. Additionally, with a validated model, we have carried out numerical experiments from which we have concluded that groundwater is a major water resource for cotton growth in this region. The capillary rise from groundwater contributes almost 23% of crop transpiration when the average groundwater depth is 1.84. m, which is the most suitable groundwater depth for this experimental site. We have concluded that cotton growth and various components of the soil water balance are highly sensitive to the groundwater table level. Different positions of the groundwater table showed both positive and negative effects on cotton growth. Likewise, cotton growth has a significant impact on the capillary rise from groundwater. As a result, groundwater is a crucial factor that needs to be considered when evaluating agricultural land management in this arid region. The updated Hydrus-1D model developed in this study provides a powerful modeling tool for evaluating the effects of the groundwater table on local land management.