Nitrate in groundwater is increasing in hilly areas of the world due to diverse land-uses and intensified anthropogenic activity. However, the key factors that control nitrate in groundwater as it leaches through the thin vadose zone are still poorly understood. In this study, the behavior of nitrate in the vadose zone during a normal year (2015) and a wet year (2016) were investigated in a cultivated farmland (FL) under wheat-maize double cropping and a field of natural vegetation (NV) in a headwater region of the Taihang Mountain. Water chemistry and N balances were quantified to estimate the accumulation and leaching of nitrate. Transport and fate of nitrate in the vadose zone were identified using stable isotopes of nitrate (δ18O-NO3−, δ15N-NO3−). Accumulation of NO3− was mainly in the shallow layer (0–50 cm) under both NV and FL in 2015. After large rain events (20–50 mm/day) during the rainy season in 2015, the leaching rates of NO3− at NV and FL sites were 86.04 and 9.61 kg/hm2, respectively. The accumulation of NO3− decreased 30% and 7% at NV and FL, respectively. However, the leaching rates of NO3− were 63.8 and 22.63 kg/hm2, and the accumulation of NO3− decreased 84% and 43% at NV and FL after extreme precipitation in 2016, respectively. Additionally, nitrate isotopes indicated that the different sources of nitrate in soil water were due to the land-use. However, nitrate isotopes showed that increased nitrate concentrations in groundwater at two sites in 2016 were due to the extreme precipitation. Accumulated high nitrate in surface soil in a normal year and leaching after extreme precipitation lead to increased nitrate concentration in groundwater, which poses a major threat in the future. The results are critical for informing land-use and water management when mitigating groundwater contamination in hilly area.