The root zone water quality model (RZWQM V.3.25) was calibrated and evaluated using four years (1993-96) of field data to simulate the effect of swine manure application on NO3-N losses with subsurface drainage water under a corn-soybean production system. The RZWQM was calibrated for corn and soybean crops separately using crop-specific calibration parameters. The main crop specific parameters of maximum nitrogen uptake rate (g/plant/day), proportion of photosynthesis to respiration, and amount of biomass (g) needed to obtain leaf area index of 1.0 were calibrated to 2.0, 0.12, 10.0 for corn and 0.5, 0.005 and 1.5 for soybean, respectively. The predicted subsurface drain flows and NO3-N concentrations in the drainage water were compared with the measured values. The predicted subsurface drain flows followed the pattern of measured drain flows, giving an average difference of about +2.0% and –9.7% for corn and soybean, respectively. The predicted NO3-N concentrations in tile water were in good agreement with the measured values for all simulation periods (overall average difference was less than 1%). The evaluation of the model for validation years (1995 and 1996) showed correlation coefficients of 0.66 and 0.57 between predicted and measured NO3-N concentrations for corn and soybean, respectively. The overall predicted NO3-N losses were within 5% of the observed NO3-N losses for both cropping systems. This shows that the crop specific parameters of the RZWQM have the potential to simulate satisfactorily the effect of crop rotation and swine manure application in alternate years and N-fixation by soybean on NO3-N losses with subsurface drain flow. To improve model performance, the crop specific parameters need to be tested for above and belowground biomass and grain yield predictions along with NO3-N losses.