Overfertilization prevails in developing apple-producing countries, but its long-term effects on regional water resources are scarcely documented. In this study, a total of 114 water samples, including groundwater, river water, and tap water, were collected from rainfed and irrigated apple-planting regions on China’s Loess Plateau. The primary objectives were to (1) systematically evaluate changes in hydrochemistry using hydrochemical indices and major ion ratios, (2) quantify NO₃⁻-N pollution and its driving factors using δ¹⁵N- and δ¹⁸O-labeled nitrate and a Bayesian isotope mixing model (MixSIAR), and (3) identify water suitable for drinking using an entropy water quality index and for irrigation by integrating electrical conductivity and Na%. All water samples contained Ca-Mg-HCO₃ facies, except for low-elevation water samples in the irrigated region with Na-HCO₃ facies. Hydrochemistry changed considerably from the 2000–2020 s in both rainfed and irrigated regions, primarily associated with agricultural activities (e.g., fertilization). Although absent in the rainfed region, NO₃⁻-N pollution was severe in the irrigated region, with 40.0 % of tap water, 25.0 % of river water, and 32.7 % of groundwater samples exceeding the World Health Organization limit of 10 mg L⁻¹. MixSIAR indicated the contribution of chemical fertilizer to NO₃⁻ was higher in irrigated than in rainfed regions, regardless of the water source. With the exception of sewage/manure-derived NO₃^–-N in the rainfed region’s groundwater, chemical fertilizer was the highest contributor to NO₃⁻-N in river water and groundwater, whereas sewage/manure was the most important nitrate source in tap water, whether irrigated or rainfed region. Regression analysis revealed N-fertilizer inputs and water level and well depths were key factors affecting groundwater NO₃⁻-N in the irrigated region compared with those in the rainfed region. Notably, all water samples in the rainfed region were suitable for drinking and irrigation, whereas in the irrigated region, 27.3 % of groundwater samples were unsuitable for drinking and 40.0 % of tap water, 75.0 % of river water, and 63.6 % of groundwater samples were doubtful-to-unsuitable for irrigation. Collectively, overfertilization in long-term apple cultivation changed regional hydrochemistry, with flood irrigation aggravating nitrate pollution and water degradation. The study provides new insights into optimum water–nitrogen management of apple production systems in China and other developing countries with similar problems.