Modification of land cover systems is being studied in subsurface drained Iowa croplands due to their potential benefits in increasing soil water and nitrogen depletion thus reducing drainage and NO3–N loss in the spring period. The objective of this study was to evaluate the impacts of modified land covers on soil water dynamics. In each individual year, modified land covers including winter rye–corn (rC), winter rye–soybean (rS), kura clover as a living mulch for corn (kC), and perennial forage (PF), as well as conventional corn (C) and soybean (S), were grown in subsurface drained plots in north-central Iowa. Results showed that subsurface drainage was not reduced under modified land covers in comparison to conventional corn and soybean. Soil water storage (SWS) was significantly reduced by PF treatments during the whole growing seasons and by kC during May through July when compared to the cropping system with corn or soybean only (p < 0.05). Treatments of rC and rS typically maintained higher SWS than C and S, respectively, during the 3 years of this study. In the spring during a 10–15-day period when the rainfall was minimal, SWS in plots with rye, kura clover, and forage decreased at a significantly higher rate than the C and S plots which were bare. Estimated evapotranspiration (ET) during this period was significantly higher in rS, kC, and PF treatments than C and S. The results of this study suggested that significantly higher ET and similar drainage for modified land covers may increase water infiltration, which would be expected to reduce surface runoff thus to decrease stream flow. Because subsurface drainage reduction was not seen in this study, impact of modified land covers on NO3–N loss needs further investigation.