Land management of agricultural crops can have impacts on soil hydrology. The objective of our research was to evaluate subsurface drain flow and soil water storage dynamics due to land management practices of select annual- and perennial-based biofuel cropping systems. The cropping systems were continuous corn (Zea mays L.; harvested for both grain and ∼50% of the corn stover) with and without a winter cereal rye (Secale cereale L. ssp. cereale) cover crop, mixed prairies (harvested annually for aboveground biomass) with and without N fertilization, and corn–soybean [Glycine max (L.) Merr.] rotations harvested only for grain. Subsurface drainage flows and soil water content profiles were continuously monitored when soils were unfrozen during 2010 through 2012. Cropping systems were evaluated based on cumulative drainage and drainage event peak flows, time lags, and total durations. Cropping system influence on soil water storage did affect subsurface drainage flow characteristics and cumulative drainage. Prairies or the use of a winter cereal rye cover crop had greater lag times by 127 to 179%, lower peak flow intensities by 23 to 36%, and lower cumulative drainage by 37 to 46% than either corn–soybean rotations or continuous corn without a cover crop. The lower cumulative drainage was attributed to greater evapotranspiration rates and lower stored soil water that resulted in a decrease in peak flow intensities and increased time lags of both peak flow and drainage initiation. Low antecedent soil moisture resulted in low peak flows and cumulative drainage. Based on these findings, prairie systems or the use of a cover crop may aid in mitigating flood frequency in subsurface-drained landscapes.