In the semi-arid tropics, productivity of soybean is around one t/ha as against achievable yields of 2.5 to 4.0 t/ha. Major constraints limiting soybean productivity are waterlogging, low rainwater use efficiency, inappropriate nutrient management practices and low soil fertility. In a long term experiment conducted at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, productivity of soybean-based systems (soybean + chickpea) and (soybean intercropped with pigeonpea) is increased to 2.5 to 3.5 t/ha through appropriate land, water, nutrient and organic matter management practices. Detailed datasets from 1996 cropping season were used for parameterization of the AquaCrop model and data from subsequent years were used for comparing the simulated and actual values. Results indicated that AquaCrop model simulated soybean yields quite well with effects of soil depth, rainfall and soil fertility status. However, model was very sensitive to initial soil moisture conditions particularly for high clay cracking soils like Vertisols and Vertic integrades. One needs to consider role of cracks in recharging the profile and suitable modifications need to be made for initializing soil moisture conditions for improving predictability of the AquaCrop model for estimating soybean yields. Results of long term experiments and simulation runs using Aqua Crop Model are discussed.