Studies quantifying winter annual cover crop effects on water quality are mostly limited to short-term studies at the plot scale. Long-term studies scaling-up water quality effects of cover crops to the watershed scale provide more integrated spatial responses from the landscape. The objective of this research was to quantify N loads from artificial subsurface drainage (tile drains) in a subbasin of the Walnut Creek, Iowa (Story county) watershed using the hybrid RZWQ-DSSAT model for a maize (Zen mays L.)soybean [Glycine max (L.) Merr.] and maize-maize-soybean rotations in all phases with and without a winter wheat (Triticum aestivum L.) cover crop during a 25-year period from 1981 to 2005. Simulated cover crop dry matter (DM) and N uptake averaged 1854 and 36 kgha(-1) in the spring in the maize-soybean phase of the 2-year rotation and 1895 and 36 kg ha(-1) in the soybean-maize phase during 1981-2005. In the 3-year rotation, cover crop DM and N uptake averaged 2047 and 44 kg ha(-1) in the maize-maize-soybean phase, 2039 and 43 kg ha(-1) in the soybean-maize-maize phase. and 1963 and 43 kg ha(-1) in the maize-soybean-maize phase during the same period. Annual N loads to tile drains averaged 29 kg ha(-1) in the maize-soybean phase and 25 kg ha(-1) in the soybean-maize phase compared to 21 and 20 kg ha(-1) in the same phases with a cover crop. In the 3-year rotation. annual N loads averaged 46, 43, and 45 kg ha(-1) in each phase of the rotation without a cover crop and 37, 35, and 35 kg ha(-1) with a cover crop. These results indicate using a winter annual cover crop can reduce annual N loads to tile drains 20-28% in the 2-year rotation and 19-22% in the 3-year rotation at the watershed subbasin scale over a 25-year period. Published by Elsevier B.V.