The Heuningnes Catchment in the Republic of South Africa was used as a case study in this research to describe the application of saltwater fraction/quantification and hydrogeochemistry methods to evaluate the extent of saline intrusion in the coastal aquifers. The argument of the research is that the presence of seawater incursion may be conclusively determined by combining the examination of the major ions, seawater fraction, stable isotopes of water, bromide, and geochemical modeling. Using stable isotopes of oxygen (18O) and deuterium (2H), major ions chemistry, seawater composition, and geochemical modeling, the genesis of salinity and mixing of different water masses were examined. Twenty-nine (29) samples of groundwater were examined. All samples showed water facies of the Na-Cl type, indicating a seawater-related origin. The significance of mixing in coastal aquifers under natural conditions was shown by the hydrogeochemical characteristics of key ions derived from ionic ratios, which demonstrated substantial adherence to mixing lines among endmembers for freshwater as well as saltwater (seawater). The quantification of seawater contribution in groundwater percentages varied from 0.01 to 43%, with three samples having concentrations of seawater above 50%. It was clear from the hydrogeochemical analysis and determination of the proportion of saltwater that the seawater intrusion impacted the coastal fresh groundwater. In addition, the chloride concentration in the groundwater ranged from 81.5 to 26,557.5 mg/L, with the corresponding δ18O values ranging from −5.5‰ to −0.9‰, which suggested that freshwater and saltwater were mixing. The Br−/Cl− ratios showed that evaporation had played a part in elevating groundwater salinity as well. Since saturation indices were below zero, the mineral dissolution could also contribute to the salinization of groundwater. Further proof of seawater incursion in the investigated catchment was supplied by geochemical modeling and bromide. Even though such tools were not verified in multiple coastal aquifers for widespread generalization, the study offered a scientifically significant understanding of the application of such tools on seawater intrusion in coastal aquifers and has useful recommendations for the aquifer setting of similar environments.