Artificial subsurface drainage is necessary to maintain agricultural production in the soils and climate of north‐central Iowa. However, it can result in adverse environmental impacts, because it intercepts and diverts some water and soluble NO3–N directly to streams. We investigated the impact of no‐till and a winter rye cover crop (Secale cereale L.) on seasonal and annual NO3–N concentration and loading in leachate from a corn (Zea mays L.)–soybean [Glycine max (L.) Merr.] rotation. The eight treatments are chisel plow (CT), chisel plow with winter cereal rye (CTr), no‐till (NT), and no‐till with winter cereal rye (NTr), with “‐C” indicating corn and “‐S” indicating soybeans. Plots with artificial subsurface drainage were monitored for water quality from 2011 to 2015. The NT and CTr treatments consistently decreased NO3–N loss on the seasonal and annual scales compared with CT. Compared with NT, NTr did not reduce NO3–N loading nor concentration in leachate, probably because of low NO3 leaching potential from NT combined with low rye cover crop biomass throughout the study with NT. The 5‐yr average annual NO3–N concentrations were: 16.9 mg L−1 with CT‐S, 16.7 mg L−1 with CT‐C, 12.6 mg L−1 with NT‐S, 12.0 mg L−1 with CTr‐S, 11.8 mg L−1 with CTr‐C, 11.4 mg L−1 with NTr‐S and NTr‐C, and 11.1 mg L−1 with NT‐C. Overall, both no‐till and a cover crop showed potential for improving N management for water quality.