We compare subsurface-drainage NO 3-N and total reactive phosphorus (TRP) concentrations and yields of select bioenergy cropping systems and their rotational phases. Cropping systems evaluated were grain-harvested corn-soybean rotations, grain- and stover-harvested continuous corn systems with and without a cover crop, and annually harvested reconstructed prairies with and without the addition of N fertilizer in an Iowa field. Drainage was monitored when soils were unfrozen during 2010 through 2013. The corn-soybean rotations without residue removal and continuous corn with residue removal produced similar mean annual flow-weighted NO 3-N concentrations, ranging from 6 to 18.5 mg N L -1 during the 4-yr study. In contrast, continuous corn with residue removal and with a cover crop had significantly lower NO 3-N concentrations of 5.6 mg N L -1 when mean annual flow-weighted values were averaged across the 4 yr. Prairies systems with or without N fertilization produced significantly lower concentrations below <1 mg NO 3-N L -1 than all the row crop systems throughout the study. Mean annual flow-weighted TRP concentrations and annual yields were generally low, with values <0.04 mg TRP L -1 and <0.14 kg TRP ha -1, and were not significantly affected by any cropping systems or their rotational phases. Bioenergy-based prairies with or without N fertilization and continuous corn with stover removal and a cover crop have the potential to supply bioenergy feedstocks while minimizing NO 3-N losses to drainage waters. However, subsurface drainage TRP concentrations and yields in bioenergy systems will need further evaluation in areas prone to higher levels of P losses.