To assess the risk that liquid swine manure (LSM) application posed to groundwater quality and determine how to manage excess nitrates, LSM pre-plant injected at 75% (LSMlow) and > 100% (LSMhigh) of corn (Zea mays L.) N requirements was compared to inorganic fertilizer (Fert), with (RC) or without (NC) a rye (Secale cereale L.) cover crop in 2 dry years (1999, 2001) and I wet year (2000) on sandy soil in Ontario. Corn yields in LSM and Fert treatments were comparable each year. When drainage potential was high, solution nitrates below the root zone in Fert (14 mg L-1) > LSM (7 mg L-1) in 1999, but in LSM (39 mg L-1) > Fert (13 mg L-1) in 2000. Occasionally in 2001, solution nitrates in LSMhigh > LSMlow and/or Fert plots, but drainage potential was low. Earlier N application in LSM (pre-plant) than Fert (77% of N sidedressed) plots in relation to rain events may have increased solution nitrates in LSM plots in 2000. Rye cover reduced solution nitrates from 8.8 mg L-1 (NC) to 4.3 mg L-1 (RC, average of all dates), regardless of nutrient source. In-season risk of NO3 leaching can be reduced by split application of N between pre-plant and sidedress, while overseeding cereal rye into standing com minimizes leaching post-harvest (fall and spring).