Abstract: Planting winter rye cover crop can reduce subsurface drainage and NO3?-N loss in corn-soybean rotation. Field data from Iowa was used to calibrate DRAINMON-N II and evaluate its applicability in cold regions in US. This study simulated the long-term (20 years) effects of winter rye cover crop on subsurface drainage and nitrogen dynamics using DRAINMOD-N II. Two treatments were set in Agricultural Drainage Water Quality-Research and Demonstration Site in Iowa. One treatment was with rye planting in winter (rye-maize-rye-soybean rotation) and the other was bare in winter (only maize-soybean). The experiments lasted for 5 years from 2005 to 2009. The drainage was collected and NO3?-N content in the drainage was measured. The DRAINMON-N II model was used for simulation of change in the drainage and NO3?-N content from 1990 to 2009. The results showed that the DRAINMON-N II model satisfactorily simulated subsurface drainage and NO3?-N loss with Nash-Sutcliffe efficiency (NSE) larger than 0.65, percent bias (PBIAS) smaller than 25%, and ratio of root mean square error to standard deviation (RSR) not larger than 0.70. Flow-weighted average NO3?-N concentration (FWANC) were simulated satisfactorily, with NSE larger than 0.50, PBIAS within 25%, and RSR not larger than 0.50. The errors between simulation and measurements of drainage and NO3?-N loss mainly reflected in March when temperature was low (average monthly temperature was -4.1 oC), which may partially cause by drainage delay. Also the larger wind speed (4 m/s) which can take away 20% of snow could affect our estimates. These results suggested that DRAINMOD-N II had good applicability in Iowa and could simulate the long-term effect of winter rye cover crop on subsurface drainage and NO3?-N loss. Long-term simulations (1990-2009) indicated that adding winter rye cover crop could reduce drainage, NO3?-N loss and FWANC by 8.1% (2.5 cm), 16.6% (6 kg/hm2, by N) and 8.6% (1 mg/L, by N), respectively. The amount of drainage was decreased year by year and the 5-yr dynamic decrement rates increased from 5% to 14%. The 5-yr dynamic NO3?-N loss varied between 4.1 and 7.3 kg/hm2, with a mean of 6.0 kg/hm2. The winter rye as a cover crop could increase evapotranspiration (ET) by 5.9% (2.6 cm), and the time period to plant cover crop also affected ET increase. When planting cover crops before soybean ET increased by 6.4%. Meanwhile, adding winter rye cover crop could increase plant uptake of nitrogen by 7.3% (10.1 kg/hm2) and nitrate fixation by 11.9% (11.3 kg/hm2). Planting winter rye could reduce net mineralization by 6.1% (10.4 kg/hm2), but it was in disagreement with the existing experiments and simulations by the other researchers. These results indicated that there is still some debate about net mineralization response to adding winter rye cover crop. Further research is necessary to understand the simulated nitrogen transport and transformation mechanisms in soil. The field data is well matched with the calibrated model, showing that the DRAINMON-N II model could reliably simulate water and nitrogen movement in the soil. This model could simulate the effect of different cropland management practices on subsurface drainage and nitrogen dynamics to optimizing cropland management practice.