In the Kirama-ara River basin, Matara, southern region of Sri Lanka, a variety of agricultural inputs are utilized, and flooding is a common hazard. Therefore, the groundwater in this area is under serious threat. But, the complete physicochemical profile of the groundwater in the Kirama-ara river basin is yet undiscovered. Therefore, the goals of this study were to (a) identify the geochemical characteristics and changes in water quality, (b) evaluate non-carcinogenic health risk and develop a Groundwater quality index (GWQI), and (c) generate a spatial distribution map for groundwater physicochemical characters in the Kirama-ara river basin in Matara, Sri Lanka. The physiochemical characteristics of 16 (G1 to G16) groundwater samples, including pH, total dissolved solids (TDS), electrical conductivity (EC), Ca2+, Mg2+, Na+, K+, Cl−, NO3−, PO43−, and SO42−, were examined for spatial and chronological variations. The pH, NO3−, and PO43− values of 50% (G1,G4,G7,G12,G13,G14,G15,G16), 6.25% (G16), and 6.25% (G16) of the samples, respectively, were determined to be exceeded the allowable limit by both the WHO and SLS standards. The physicochemical investigation demonstrated that while 87.5% of the locations were acceptable for drinking, 12.5% of them lacked sufficient amounts. The most common hydro-chemical facies were Ca2+-Mg2+-HCO3−, mixed Ca2+-Mg2+-Cl− face, and Ca2+-Cl−. Rock weathering has a weighty effect on the ionic composition and chemistry of groundwater in the study area. Additionally, health risk assessment revealed that children face greater health risks than adults. Further investigations should be conducted to build reasonable management plans for long-term groundwater quality conservation and public health.