Integrated crop–livestock rotations enhance biodiversity and ecosystem services, but more information is needed on potential nutrient pollution from these systems. We evaluated nitrate and phosphorus in subsoil water (1‐m depth) from the first 2 yr of a 5‐yr organic crop rotation that incorporated goats (Capra aegagrus hircus) on pasture. The rotation consisted of the following yearly phases: (a) corn (Zea mays L.), (b) soybean [Glycine max (L.) Merr.], (c) pasture Year 1, (d) pasture Year 2, and (e) pasture Year 3 (not reported). Each yearly phase was represented every year of the study. Reference plots in continuous perennial pasture without animals and continuous corn–soybean were also included. Significantly greater nitrate concentrations were observed under cropped plots compared with pasture plots, whereas phosphorus concentrations were significantly greater under pasture plots. Differences were most pronounced at the end of the growing season. For example, in November 2019, cropped plots averaged 13.9 mg nitrate L–1 and 0.28 mg phosphorus L–1 compared with 2.4 mg nitrate L–1 and 0.62 mg phosphorus L–1 under pasture. Goats had no impact on nitrate or phosphorus in subsoil water. Year‐round plant nutrient uptake by established root systems may have contributed to lower nitrate under pasture plots. Phosphorus leaching may have occurred via preferential macropore flow and was likely influenced by high native soil phosphorus concentrations. In cropped plots, tillage may have influenced nitrate concentrations through mineralization of nitrogen associated with soil organic matter, while also disrupting macropore channels and thus reducing phosphorus transport to subsoil water.