The deep-rooted economic trees decrease water storage but increase nitrate-nitrogen (NO3–N) accumulation in the soil due to the root water uptake and excessive use of fertilizers. Knowing how the NO3 accumulates in the soil and to what extent it can be flushed out or transformed can provide insights on the processes controlling N flux to waterways. We sampled cultivated farmland and orchards with varying ages of apple and peach trees in the loess deposits to > 15 m depth to measure the contents and isotopes of water and NO3 in soils. The novelty of this study is that the water isotopes are used to analyze water and NO3 transport, while the NO3 isotopes are further employed for NO3 source and transformation analysis. The parabolic NO3–N profiles (258–3579 kg N ha−1) were mainly observed within 0–5 m under different land use types. The surface-aggregated NO3 reservoirs under old apple orchard were about six times of farmland due to the overuse of chemical fertilizers, while those of peach orchard were only half of farmland because of less fertilizer inputs and possible root absorption effects. Piston flow resulted in the overall slow water movement and low NO3 flux under different land use types in deep loess deposits. Despite the soil water recharge by precipitation and low surface evaporation, the strong transpiration effects further resulted in no water and NO3 fluxes in the deep layers under old apple orchard. Nitrate reservoirs were mainly contributed by soil organic N (44 % ± 26 %) and ammonium N fertilizer (36 % ± 20 %), but their transformation was dominated by nitrification under old apple orchard and by mineralization in deep layers. The risks of NO3 bombs are temporarily weakened by lower dried soil layers under deep rooted plants; however, with lower water movement rates and limited denitrification potential, NO3 would eventually reach the aquifers in a few hundred years or more. This study provides new insights for clarifying NO3 transport and transformation processes by combing multiple isotopes, and the NO3 bombs would chronically endanger the sustainable development of terrestrial ecosystems and the environment in arid regions.