In an effort to determine the reason behind excellent nitrate remediation capacity at Kelantan region, a multivariate approach is employed to evaluate extent to which the influence of sea on soil geochemical composition affect variation pattern of groundwater quality. The results obtained from geochemical analysis of paleo-beach soil in coastal site at Bachok revealed multiple redox activity at different soil strata, involving both heterotrophic and autotrophic denitrification. In soil and water analysis, eight of the fourteen hydro-geochemical parameters (conductivity, temperature, soil texture, oxidation reduction potential, pH, total organic carbon, Fe, Cu, Mn, Cl−, SO42−, NO2−, NO3− and PO43−) measured using standard procedures were subjected to multivariate analysis. Evaluation of general variation pattern across the area reveals that the principal component analysis (PCA), hierarchical cluster analysis (HCA) and linear discriminant analysis (LDA) are in consonance with one another on apportioning three parameters (SO42−, Cl− and conductivity) to the coastal sites and two parameters (Fe and NH4+ or NO3−) to inland sites. The step forward analysis of LDA reveals four parameters in order of decreasing significance as Cl−, Fe and SO42−, while the two-way HCA identifies three clusters on location basis, respectively. In addition to the significant data reduction obtained, the results indicate that proximity to sea and location/geological-based influence are more significant than temporal-based influence in denitrification. By extension, the research reveals that influence of labile portion of natural resources is explorable for broader application in other remediation strategies.