A hydrogeochemical relation has been hypothesized through the analyses of physiochemical data of a fractured volcanic rock aquifer located in the Lower Baringo Basin, Kenyan Rift. Data sets included 15 individual metrics determined in 42 dry and wet season water samples obtained from 6 boreholes in the area. Aquifer evolutionary theory was postulated using sequential principal component analysis (PCA) and hierarchical cluster analysis. To eliminate the effects of scale dimensionality, PCA decomposed the variable data into 4 factors, namely, electrical conductivity, salinity, alkalinity, and carbonate equilibrium with external pH control for the dry season and salinity, carbonate equilibrium with external pH control, alkalinity, and electrical conductivity for the wet season. The main result depicted a major shift in the variability factor from electrolytic conductivity (34.8%) in the dry season to salinity (23.5%) in the wet season. Ward’s linkage cluster analysis partitioned the aquifer into 2 spatially discrete associations; the western and the eastern entities, respectively, in spite of their shared recharge area. These agglomerative scheduling validated in an integrative approach (with groundwater flow predictions using a calibrated petrophysical groundwater model for the area) linked the 4 factors to aquifer processes and 3 pathways: fault permeability, weathering processes, and water-rock interaction. Statistical approaches are, therefore, useful in the conceptualization of pollutant sources and their attenuation for effective groundwater quality management.