The chemical composition of groundwater is the product of the evolution and incorporation of major ions, the product of natural hydrogeochemical processes or human interference that occurs in an aquifer. To establish the hydrogeochemical groundwater characteristics and suitability, 47 samples were collected from shallow wells in the study area. The objective was to determine the hydrogeochemical assessment of the groundwater in the shallow aquifer and establish the water quality and pollution associated with the dissolved organic matter in the San Luis Potosí sub-basin. The water quality assessment has been carried out by evaluating the physicochemical parameters such as temperature, pH, EC, TDS, and the main ions, which present the following trend: Ca2+>Na+>K+>Mg2+, HCO3− > SO42− > Cl− > NO3. The type of water in the area is mainly of four types: Ca–Na–HCO3–Cl (32%), Ca–Na–SO4–HCO3 (19%), Na–Ca–HCO3–Cl (13%), Ca–Na–HCO3–SO4 (11%). The content of NO3− (4.0–50.0 mg L−1), NH4+ (0.03–40.0 mg L−1), SO42− (20.0–276.0 mg L−1) y PO43− (0.01–45.5 mg L−1) indicate contamination that may come from inorganic and organic matter. Organic matter of anthropogenic origin was identified by 3D fluorescence. The results of this study demonstrate that the main processes that affect and control the chemical composition of the water in the shallow aquifer of SLP are silicate weathering, albite weathering, and reversible ion exchange.