Hydrogeochemical processes and quality assessment for shallow groundwater are pivotal issues to be solved in many regions over the world due to the easy access of shallow groundwater. In this study, eighty-six water samples were collected from shallow aquifers of Chongqing, China, during July–September 2019. Multivariate statistical techniques, major ion ratios, and geochemical modeling were integrated to investigate hydrogeochemical characteristics and controlling factors. Afterwards, groundwater quality in spatial was classified by entropy-weighted water quality index and geographic information system (GIS) spatial analysis. Groundwater samples were alkaline and possessed high total dissolved solids (TDS) values. Two-group samples were distinguished as mix cations-HCO3-SO4 (group 1) and Ca-Mg-SO4 (group 2) facies. Hydrogeochemical compositions of group 1 samples were dominated by silicate dissolution and ion exchange, while sulfate and calcite dissolution were the main factors influencing the hydrogeochemical characteristics of group 2. The overall quality of groundwater samples varied greatly from excellent quality to extremely poor quality. Group 1 samples were found with excellent and good quality and suitable for drinking purposes. Group 2 samples were all unsuitable for direct drinking purposes as the quality varied from medium to extremely poor, but were spatially limited. Groundwaters with relatively poor quality were due to dissolution of sulfate that were locally enriched in the aquifers. The new findings of this study are expected to provide the reference for future management and sustainable exploitation of groundwater in Chongqing.