An increasing number of farmers are beginning to use cover crops to improve their soil productivity. There is also growing interest from policy makers to use winter cover crops as a strategy to reduce or buffer the negative impacts of agricultural systems and climate variability on soil, water and air quality in the Midwest.  The objective of this study is to utilize a cropping systems model to improve understanding of soil water dynamics and predict subsequent benefits (ie: reduced nitrate losses and drainage) and tradeoffs (ie: impacts to cash crop yields) associated with cover crop management.  APSIM (Agricultural Production Systems sIMulator) has been successfully utilized in recreating dynamics of corn-soybean rotations using Iowa meteorological and soil data.  We conducted model calibration for a corn-soybean-winter rye cover crop research plot in Central Iowa with more than ten years of historical information (yield data, soil nitrogen, soil moisture and drainage).  APSIM captured soil water dynamics at three depths over a series of wetter, drier and average precipitation years.  Predicted biomass and yields are within the range of  observed values over a 13 year period.  Through simulations, we estimated the long-term cover crop effects on nitrate leaching, soil water dynamics, and cash crop yields.