Shallow water table (WT) influences crop growth and production in many major agricultural regions across the globe. We enhanced the APSIM-soybean model to accurately simulate root depth in fields with shallow water tables. We used data from a controlled experiment (Rhizotron facilities) that included root depth observations for nine WT treatments to develop and calibrate the new model. Analysis indicated that unconstrained root growth occurs until volumetric soil moisture approaches 0.03 mm/mm below saturation. Below that threshold, root growth linearly decreases to zero at saturation. Inclusion of this factor into the model increased accuracy of root depth simulations from R2 of 0.65 to 0.97 and reduced root mean square error from 45 to 9 cm. Validation of root depth simulations using independent field data from Iowa, USA (years 2016, 2017, 2018) confirmed the model. We also found that the inhibition of root growth in response to shallow WT substantially impacted the vertical distribution of the roots in both measurements and simulations. Overall, this work enhances the capability of APSIM in simulating production and environmental aspects of cropping systems, especially in regions with shallow water tables typical of the Corn Belt, USA.