This study evaluated the relationship between water pH and the physicochemical properties of water while controlling for the influence of heavy metals and bacteriological factors using a nested logistic regression model. The study further sought to assess how these relationships are compared across confined water systems (ground water) and open water systems (surface water). Samples were collected from 100 groundwater and 132 surface water locations in the Tarkwa mining area. For the zero-order relationship in groundwater, EC, TDS, TSS, Ca, SO42-, total alkalinity, Zn, Mn, Cu, faecal and total coliform were more likely to predict optimal water pH. For surface water however, only TSS, turbidity, total alkalinity and Ca were significant predictors of optimal pH levels. At the multivariate level for groundwater, TDS, turbidity, total alkalinity and TSS were more likely to predict optimal water pH while EC, Mg, Mn and Zn were associated with non-optimal water pH. For the surface water system, turbidity, Ca, TSS, NO3, Mn and total coliform were associated with optimal water pH while SO42-, EC, Zn, Cu, and faecal coliform were associated with non-optimal water pH. The non-robustness of predictors in the surface water models were conspicuous. The results indicate that the relationship between water pH and other water quality parameters are different in different water systems and can be influenced by the presence of other parameters. Associations between parameters are steadier in groundwater systems due to its confined nature. Extraneous inputs and physical variations subject surface water to constant variations which reflected in the non-robustness of the predictors. However, the carbonate system was influential in how water quality parameters associate with one another in both ground and surface water systems. This study affirms that chemical constituents in natural water bodies react in the environment in far more complicated ways than if they were isolated and that the interaction between various parameters could predict the quality of water in a particular system.