Quantifying the impacts of soil disturbance on crop yield after installing an underground pipeline is essential for implementing effective mitigation plans and land restoration guidelines in agricultural systems. The objective of this study was to model maize and soybean yields on disturbed (subsurface pipeline installation areas) and adjacent undisturbed (control) land areas. Field observations and simulation results depicted the negative impacts of soil disturbance on soil physical, chemical, and hydrological properties. Grain yield and aboveground biomass losses up to 27% were observed in the pipeline disturbed area, where the soil profile had 15% lower plant-available water retention capacity than the undisturbed soil. APSIM was parameterized using two years (2019 and 2020) of in-season crop growth observations from a soybean-maize rotation system. Simulation of yield production was further evaluated against independent data from 2017 to 2018. The overall model performance was assessed using the index of modeling efficiency (EF). The model was effective in simulating aboveground biomass (EF disturbed-undisturbed: 0.96–0.98), grain yield (EF disturbed-undisturbed: 0.91–0.96), and soil water content in the 0–450 mm soil layer (EF disturbed-undisturbed: 0.84–0.86) for the parameterization dataset. Furthermore, the EF values for simulations of the independent yield data were also satisfactory (EF of 0.98 and 0.97 for disturbed and undisturbed soils, respectively). Soil disturbance reduced water use efficiency (WUE) by 25% and 30% in soybean and maize, respectively. This study indicated the suitability of using APSIM for simulating crop growth and yield production in the highly disturbed pipeline installation area.