Crop rotation and cultural practice may influence soil residual N available for environmental loss due to crop N uptake and N immobilization. We evaluated the effects of stacked vs. alternate-year crop rotations and cultural practices on soil residual N (NH4-N and NO3-N contents) at the 0–125 cm depth, annualized crop N uptake, and N balance from 2005 to 2011 in the northern Great Plains, USA. Stacked rotations were durum (Triticum turgidum L.)–durum–canola (Brassica napusL.)–pea (Pisum sativum L.) (DDCP) and durum–durum–flax (Linum usitatissimum L.)–pea (DDFP). Alternate-year rotations were durum–canola–durum–pea (DCDP) and durum–flax–durum–pea (DFDP). Both of these are legume-based rotations because they contain legume (pea) in the crop rotation. A continuous durum (CD) was also included for comparison. Cultural practices were traditional (conventional tillage, recommended seeding rate, broadcast N fertilization, and reduced stubble height) and improved (no-tillage, increased seeding rate, banded N fertilization, and increased stubble height) systems. The amount of N fertilizer applied to each crop in the rotation was adjusted to soil NO3-N content to a depth of 60 cm observed in the autumn of the previous year. Compared with other crop rotations, annualized crop biomass N was greater with DCDP and DDCP in 2007 and 2009, but was greater with DDFP than DCDP in 2011. Annualized grain N was greater with DCDP than CD, DFDP, and DDFP and greater in the improved than the traditional practice in 2010 and 2011. Soil NH4-N content was greater with CD than other crop rotations in the traditional practice at 0–5 cm, but was greater with DDCP than CD and DDFP in the improved practice at 50–88 cm. Soil NO3-N content was greater with CD than other crop rotations at 5–10 cm, but was greater with CD and DFDP than DCDP and DDCP at 10–20, 88–125, and 0–125 cm. Nitrate-N content at 88–125 and 0–125 cm was also greater in the traditional than the improved practice. Nitrogen balance based on the difference between N inputs and outputs was greater with crop rotations than CD. Increased N fertilization rate increased soil residual N with CD, but legume N fixation increased N balance with crop rotations. Legume-based crop rotations (all rotations except CD) reduced N input and soil residual N available for environmental loss, especially in the improved practice, by increasing crop N uptake and N immobilization compared with non-legume monocrop.