Utilization of cereal rye (Secale cereale L. ssp. cereal) as a winter cover crop has potential benefits for subsurface drainage and NO3 loss reduction. The objective of this study was to quantify the soil water balance components and impacts of a rye cover crop on subsurface drainage in central Iowa. Rye was planted in lysimeters in mid-October and terminated in early June in 3 yr and the lysimeters were left fallow during the summer months. Subsurface drainage water was generally pumped out weekly along with taking soil moisture measurements; however, multiple appreciable rain events in a given week required more frequent pumping. During May through July of the 3 yr, monthly subsurface drainage was significantly reduced by 21% when comparing the rye system to bare soil (P < 0.1). Drainage of individual pumping events was significantly lower in the rye lysimeters than the bare lysimeters when averaged across 3 yr (P < 0.05). Soil water storage in the rye treatment was also significantly lower than the bare treatment (P < 0.05) in all 3 yr. The winter cover crop effectively reduced subsurface drainage, which would then be expected to decrease the NO3 load, which is essential to water quality improvement. During the main growing month, May, estimated evapotranspiration of rye was 2.4 mm d−1, significantly higher than evaporation from the bare treatment (1.5 mm d−1, P < 0.1). Soil water depletion by rye in May could reduce the drainage volume and may also help facilitate trafficability, but it is still unknown what impact there may be on crop production in dry years.