The Agricultural Production Systems Simulator (APSIM) is a key tool to identify agricultural management practices seeking to simultaneously optimize agronomic productivity and input use efficiencies. The aims of this study were to validate APSIM for prediction of stover and grain yield of corn in four contrasting soils with varied N fertilizer applications (156–269 kg N ha−1) and to predict timing and volume from artificial subsurface drains in continuous corn and corn-soybean rotations in a silty clay loam soil at West Lafayette, IN. The APSIM validation was carried-out using a long-term dataset of corn stover and grain yields from the North Central Region of IN. The CCC (Concordance Correlation Coefficient) and SB (Simulation Bias) were used to statistically evaluate the model performance. The CCC integrates precision through Pearson’s correlation coefficient and accuracy by bias, and SB indicates the bias of the simulation from the measurement. The model demonstrated very good (CCC = 0.96; SB = 0%) and satisfactory (CCC = 0.85; SB = 2%) ability to simulate stover and grain yield, respectively. Grain yield was better predicted in continuous corn (CCC = 0.73–0.91; SB = 19–21%) than in corn-soybean rotations (CCC = 0.56–0.63; SB = 17–18%), while stover yield was well predicted in both crop rotations (CCC = 0.85–0.98; SB = 1–17%). The model demonstrated acceptable ability to simulate annual subsurface drainage in both rotations (CCC = 0.63–0.75; SB = 2–37%) with accuracy being lower in the continuous corn system than in corn-soybean rotation system (CCC = 0.61-0.63; SB = 9–12%). Daily subsurface drainage events were well predicted by APSIM during late spring and summer when crop water use was high, but under-predicted during fall, winter and early spring when evapotranspiration was low. Occasional flow events occurring in summer when soils were not saturated were not predicted by APSIM and may represent preferential flow paths currently not represented in the model. APSIM is a promising tool for simulating yield and water losses for corn-based cropping systems in north central Indiana US.