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The Heihe River Basin (HRB) is an inland watershed in northwest China with a total area of approximately 130,000 km(2), stretching from the Qilian Mountains in the south to the oases and agricultural fields in the middle and further to the Gobi desert in the north bordering Mongolia. As part of a major ecohydrological research initiative to provide a stronger scientific underpinning for sustainable water management in arid ecosystems, a regional-scale integrated ecological and hydrological model is being developed, incorporating the knowledge based on the results of environmental isotope tracer analysis and the multiscale observation datasets. The first step in the model development effort is to construct and calibrate a groundwater flow model for the middle and lower HRB where the oases and vegetation along the Heihe river corridor are highly dependent on groundwater. In this study, the software tool Arc Hydro Groundwater’ is used to build and visualize a hydrogeological data model for the HRB that links all relevant spatiotemporal hydrogeological data in a unified geodatabase within the ArcGIS environment. From the conceptual model, a regional-scale groundwater flow model has been developed using MODFLOW-2005. Critical considerations in developing the flow model include the representation of mountainous terrains and fluvial valleys by individual model layers, treatment of aquifer heterogeneities across multiple scales and selection of proper observation data and boundary conditions for model calibration. This paper discusses these issues in the context of the Heihe River Basin, but the results and insights from this study will have important implications for other large, regional groundwater modelling studies, especially in arid and semiarid inland river basins. Copyright (c) 2014 John Wiley & Sons, Ltd.