Artificial subsurface drainage in cropland creates pathways for nutrient movement into surface water; quantification of the relative impacts of common and theoretically improved management systems on these nutrient losses remains incomplete. This study was conducted to assess diverse management effects on long-term patterns (1998-2006) of NO, NH, and PO loads (). We monitored water flow and nutrient concentrations at subsurface drains in lysimeter plots planted to continuous corn ( L.) (CC), both phases of corn-soybean [ (L.) Merr.] rotations (corn, CS; soybean, SC), and restored prairie grass (PG). Corn plots were fertilized with preplant or sidedress urea-NHNO (UAN) or liquid swine manure injected in the fall (FM) or spring (SM). Restored PG reduced NO eightfold compared with fields receiving UAN (2.5 vs. 19.9 kg N ha yr; < 0.001), yet varying UAN application rates and timings did not affect NO across all CCUANs and CSUANs. The NO from CCFM (33.3 kg N ha yr) were substantially higher than for all other cropped fields including CCSM (average 19.8 kg N ha yr, < 0.001). With respect to NH and PO, only manured soils recorded high but episodic losses in certain years. Compared with the average of all other treatments, CCSM increased NH in the spring of 1999 (217 vs. 680 g N ha yr), while CCFM raised PO in the winter of 2005 (23 vs. 441 g P ha yr). Our results demonstrate that fall manuring increased nutrient losses in subsurface-drained cropland, and hence this practice should be redesigned for improvement or discouraged.