Heavily fertilized and irrigated apple orchards on China's Loess Plateau may contribute to regional groundwater nitrate pollution. To examine the groundwater pollution risk, we analysed moisture and nitrate in deep soil profiles in cropland and different aged apple orchards and nitrate in groundwater in conventionally and excessively irrigated orchards. Compared with cropland, conventionally irrigated apple orchards had higher moisture at 0-6 m but also a desiccation layer at 6.4-11 m. Regression analysis predicted desiccation would first appear at 14-yr apple orchards. Excessive irrigation did not eliminate the desiccation layer, and its thickness increased with stand age. Residual soil nitrate was significantly higher in orchards than in croplands. Soil NO3--N content stabilized at increasing depth with increasing stand age. Low NO3--N concentrations at depth and dual isotope comparisons of delta 15N-NO3- and delta 18O-NO3- indicated that 13 m was a sufficient depth to evaluate soil NO3-- N in irrigated apple orchards. Groundwater NO3--N was much lowers in conventionally than in excessively irrigated apple orchards. According to a MixSIAR isotope mixing model, synthetic N fertilizer was the greatest contributor to groundwater NO3--N. Soil NO3--N was predicted to pollute groundwater at 38 years. Thus, fertilization and irrigation must be optimized to eliminate soil desiccation, reduce nitrate surplus, and protect groundwater.