Water quality and quantity should be paid more attentions for regions with arid climate and thick vadose zones since the limited groundwater cannot be replenished rapidly once polluted. This study focused on the Loess Plateau of China to investigate the geochemical mechanism affecting groundwater chemistry and to calculate contribution rates of multiple sources to groundwater solutes. We employed multiple methods (diagrams, bivariate analyses, hierarchical cluster analysis (HCA), sodium adsorption ratio (SAR), water quality index (WQI), correlation analysis, forward simulation) for the above purposes. We collected 64 groundwater samples in the thick loess deposits in June 2018 (flood season) and April 2019 (dry season). The average concentrations of cation were in the order of Ca2+ > Na+ > Mg2+ > K+ in the flood season, and Na+ > Ca2+ > Mg2+ > K+ in the dry season. The order of anions contents in the flood season and the dry season was HCO3− > SO42− > Cl− > NO3−. The major hydrochemical facies were Ca-HCO3 and Ca·Mg-HCO3 in the flood season, and Na·Ca-HCO3·SO4 and Na-HCO3 in the dry season, respectively. Most of the groundwater (95% in the flood season and 96% in the dry season) was suitable for drinking, and overall water quality (except samples F28 and D13) was acceptable for irrigation. Mineral dissolution and cation exchange were important natural processes affecting groundwater chemistry. A forward model showed that the contribution of atmospheric input, anthropogenic input, evaporite dissolution, silicate weathering and carbonate weathering to solutes in groundwater was 2.3 ± 1.5%, 5.0 ± 7.1%, 19.3 ± 21.4%, 42.8 ± 27.3% and 30.6 ± 27.1% in the flood season, and 9.1 ± 6.4%, 3.4 ± 5.2%, 20.3 ± 15.9, 56.6 ± 23.2%, and 10.7 ± 15.4% in the dry season, respectively. Although the overall contribution of anthropogenic inputs was minor, it was the dominant source of solutes for some groundwater samples. This study provides fundamental information for water management in arid areas.