Subsurface drainage, a water management practice used to remove excess water from poorly drained soils, can transport substantial amounts of NO3 from agricultural crop production systems to surface waters. A field study was conducted from the fall of 1986 through 1994 on a tile-drained Canisteo clay loam soil (fine-loamy, mixed, superactive, calcareous, mesic Typic Endoaquoll) to determine the influence of time of N application and use of nitrapyrin [NP; 2-chloro-6-(trichloromethyl) pyridine] on NO3 losses from a corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] rotation. Four anhydrous ammonia treatments [fall N, fall N + NP, spring preplant N, and split N (40% preplant and 60% sidedress)] were replicated four times and applied at 150 kg N ha(-1) for corn on individual drainage plots. Sixty-two percent of the annual drainage and 69% of the annual NO3 loss occurred in April, May, and June. Flow-weighted NO3-N concentrations in the drainage water were two to three times greater in the two years following the three-year dry period compared with preceding and succeeding years. Nitrate N concentrations and losses in the drainage from corn were greatest for fall N with little difference among the other three N treatments. Nitrate losses from soybean were affected more by residual soil NO3 following corn than by the N treatments per se. Averaged across the four rotation cycles, flow-normalized NO3-N losses ranked in the order: fall N > split N > spring N = fall N + NP. Under these conditions NO3 losses from a corn-soybean rotation into subsurface drainage can be reduced by 13 to 18% by either applying N in the spring or using NP with late fall-applied ammonia.