Hydrogeochemical surveys were conducted in parts of the Proterozoic Shillong basin in Meghalaya to locate the unconformity-related uranium deposits, related alteration patterns, and the influence of the rock formations on the groundwater solute chemistry. Shillong Basin comprises Proterozoic metasediments and felsic volcanics of Tyrsad Formation, undeformed arenaceous Barapani Formation with intrusive granites, and metabasic sills and dykes. The groundwater quality is determined for drinking, and domestic-agro-industrial utilities using hydrogeochemical tools and physicochemical parameters. The water is acidic to slightly alkaline and has an oxidizing redox environment, Electrical Conductivity (EC), Total Dissolve Solids (TDS), and major ions fell below the World Health Organization (WHO) and Indian Standards Institute (ISI) acceptable limits except for Zn, Fe, and SiO2 showing higher concentrations.The sequences of abundance of major cations and trace elements are Fe>Zn>SiO2>Ca2+>Na+ >Mg2+>K+ >U and anions as HCO3>Cl- >SO4 2- .Groundwater character was assessed by ion exchange, simple dissolution, and unusual dissolution mechanisms. The area has dominant CaHCO3, NaHCO3, and restricted CaMgHCO3 type water. Plagioclase dissolution and high SiO2 and cation exchange of Ca for Na were identified. The groundwater indices of Sodium Percent, Kelley’s Index, Sodium Adsorption Ratio, Magnesium Ratio, Electrical Conductivity, TDS, USSL, and Wilcox index were found suitable for agro-industrial uses. Permeability Index is found to be suitable in most areas and the Corrosivity Ratio shows the areas of galvanized pipes and PVC pipes to be used for water supply. AHC analysis shows three distinct groups of water types, as well as the factor analysis, also shows the three prominent factors of water types defining the dimensionality of water types. Magnesium metasomatic alteration zones and Zn anomalous zones are delineated.