Identifying the environmental factors controlling deep soil water and nitrate is important for the sustainability of vegetation and ecosystems. However, the combined effects of multiple factors at varying scales have been poorly understood, especially in those regions with thick vadose zones and deep-rooted plants. The aim of this study is to identify the multivariate controls of water and nitrate in seven > 13 m deep boreholes under different land use types on China’s Loess Plateau. After measuring soil water and nitrate contents, the combined effects of climatic factors (precipitation, temperature, and potential evapotranspiration) and soil properties (soil texture, magnetic susceptibility, pH, EC, and soil organic carbon) were explored by wavelet analysis. Land use is the key factor regulating deep soil water and nitrate reservoirs, with high water deficit and low nitrate accumulation within 0–10 m under non-fertilized forestlands and shrublands. The positive and negative standardized ratios respectively suggested the synergistic and antagonistic relationships of water and nitrate under shallow- and deep-rooted vegetation. As the important agent for nitrate leaching, soil water is influenced by magnetic susceptibility and sand. Furthermore, soil water, pH, EC, and soil organic carbon are individually or simultaneously responsible for nitrate transport and transformation, especially at large scales (> 7.5 m). This study provides novel insights for vegetation and environmental management, and benefits the parameterizing of process-based hydrological and biogeochemical models at regional or global scales, especially in the deep unsaturated zones.