Understanding the behavior of nitrate in the unsaturated zone is critical for predicting groundwater nitrate pollution. Although this issue has been intensively investigated for shallow soil profiles, it remains poorly understood in deep soils. We collected soil samples up to 20 m depth under farmland and apple orchards with trees that were 16 and 22 years old (A16 and A22). We then determined soil-water content, stable isotopes (δ2H and δ18O) and nitrate content under two land use types. The stable isotopes of nitrate under two apple orchards were measured to a depth of 16 m. The mean nitrate contents in the shallow soils (0–6 m) under apple orchards (78.8 ± 87.8 mg kg−1 for A16, 180 ± 155 mg kg−1 for A22) were significantly higher than that of farmland (2.40 ± 1.56 mg kg−1) (p < 0.01), whereas the nitrate contents in the deep soils (6–20 m) were almost similar between apple orchards and farmland. Ammonium or urea-based nitrogen (N) fertilizers (30–61%) were the predominant contributors to nitrate in the shallow soil layers, followed by soil organic N and manure & sewage, whereas the soil organic N (mean 34%) was the primary source of nitrate in deep soils. Isotopic data revealed that the N transformation was controlled by nitrification, and denitrification was not apparent throughout the soil profiles. The downward transport of nitrate lagged behind soil-water. Nitrate was leached by piston flow in the vadose zone, and the nitrate from N application since the 1980 s has only infiltrated to 6 m depth. The difficulty in recharging deep soils mitigates the transport of nitrate to lower depths. The combination of water-nitrate stable isotopes provides new insights for identifying nitrate sources, transformation, and transport in the thick unsaturated zone.

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