Nitrate accumulated deep (>100 cm) in the regolith (soil and saprolite) threatens groundwater quality, but most studies focus only on nitrate nearer the surface (<100 cm). Surface soil management versus regolith interactions affect deep nitrate leaching, but their combined impact remains unclear. This study measured how deep nitrate accumulation was affected by crop practices including orchard/cropland planting years, regolith structure, and soil properties in highly weathered subtropical red soils. Deep nitrate storage varied from 43.6 to 1116.3 kg ha-1. Regolith thickness was positively correlated with nitrate storage (R2 = 0.43, p < 0.05). Reticulated red clay (110-838 cm) had 81% of the accumulated nitrate and overlapped with 79% of the nitrate accumulation layer. All of the nitrate accumulation parameters (except for peak depth (PD)) generally increased with the planting years. The difference in peak nitrate concentration (9.0-20.0 mg kg-1) with planting year gradient (3-58 years) varied by 2.2 times, and the difference in nitrate storage (43.6-425.7 kg ha-1) varied by 9.8 times. Texture and pH explain 41.6% of the variation in nitrate concentration. As soil management practices interact with deeper regolith to control the spatial pattern of nitrate accumulation, vulnerable regions could be identified to avoid high accumulation.