In this study, the surface charge properties of perfluorinated C8 (PerfluoroC8) and undecanoic acid (UDA) modified silica hydride stationary phases have been investigated. The zeta potential values of these stationary phases were measured in aqueous/acetonitrile mobile phases of different pH, buffer concentrations and acetonitrile contents. The retention behaviour of several basic, acidic and neutral compounds were then examined with these two stationary phases, with U-shaped retention dependencies evident with regard to the organic solvent content of the mobile phase. Plots of the logarithmic retention factor versus buffer concentration revealed slopes ≥ −0.41 for both stationary phases, indicating the involvement of mixed mode retention mechanisms with contributions from both ionic and non-ionic interactions. Using a linear solvation energy relationship approach, the origins of these interactions under different mobile phase conditions were differentiated and quantified. The PerfluoroC8 stationary phase exhibited stronger retention for basic compounds under high acetonitrile content mobile phase conditions, whilst stronger retention was observed for all compounds with the UDA stationary phase under high aqueous content mobile phase conditions. The more negative zeta potentials of the UDA stationary phase correlated with higher total charge density, surface charge density and charge density at the beta plane (the outer plane of the double layer) compared to the PerfluoroC8 stationary phase. With mobile phases of low buffer concentrations, more negative zeta potential values were unexpectedly observed for the PerfluoroC8 stationary phase with slight increases in the C descriptor value, reflecting also the greater accessibility of the analytes to the stationary phase surface. Comparison of the retention behaviours on these phases with other types of silica hydride stationary phases has revealed different patterns of selectivity.