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Nitrogen (N) fertilizer enhances crop production, but field runoff impacts water quality in adjacent freshwaters. Planting winter cover crops reduces nitrate-N losses during the fallow period, but less is known about impacts on ammonium-N. From 2016–2023, we sampled biweekly from the Shatto Ditch and Kirkpatrick Ditch Watersheds in Indiana (USA) to compare the impact of cover crops on dissolved inorganic nitrogen at the field-, edge-of-field, and watershed-scales. We measured soil ammonium-N and nitrate-N, biomass, and organic matter in fall and spring. Cover crops reduced soil ammonium-N at Shatto and soil nitrate-N in both watersheds. Tile losses and watershed yields of ammonium-N occurred on scales orders of magnitude lower than nitrate-N. Tile ammonium-N losses from cover cropped fields ranged from 97 % lower to 31 % higher at Shatto, and 45 % lower to 75 % higher at Kirkpatrick compared to those without. Cover crops reduced field-scale nitrate-N losses at Shatto by 58–87 %, but losses at Kirkpatrick ranged 99 % lower to 15 % higher. Tile flow explained interannual variation in nitrate-N losses, while field-scale ammonium-N losses were driven by soil and microbial interactions and mobilization during storms. Watershed-scale ammonium-N and nitrate-N yields correlated with runoff (Kendall τ=0.45 and 0.39, respectively). While nitrate-N yields mirrored runoff, ammonium-N yields exhibited a step-functional increase, pointing to the importance of storms as a driver of loss. As Midwest crop production adapts to fluctuating environmental conditions, we demonstrate how applying cover crops over a multi-year period can mitigate ammonium-N losses