The active sites of mineral surfaces play an important role in many industrial processes, such as mineral flotation and dewatering. This paper was aimed to investigate the effect of Al- and Si-active sites on the mineral crystal faces exposed to water on the electrokinetic properties, surfactant adsorption, and floatability of diaspore and kaolinite, which are, respectively, the valuable and gangue minerals in the processing of diasporic bauxite ores. Specifically, the acid treatment was used to change the physicochemical properties of diaspore and kaolinite minerals for their selective flotation. Microelectrophoresis method was used to determine the zeta (surface) potential of diaspore and kaolinite particles before and after the acid treatment as a function of pH. The change in the surface potential was analyzed applying the theory on the electrical double layers at the solid-solution interface. The proton donor acceptor reactions occurring simultaneously on amphoteric alumina or/and silica sites of diaspore and kaolinite were considered. The mass balances were applied to link the surface active sites with the minerals charge and potential. Comparing the modeling with the experimental data revealed the significant decrease in the Al-active sites and increase in the Si-active sites by the acid treatment. Single mineral flotation and surfactant adsorption tests of diaspore and kaolinite before and after the acid treatment were carried out using sodium hexametaphosphate (HMP) and dodecylamine hydrochloride (DAH) as a depressant and a collector, respectively. After the acid treatment, the adsorption density of depressant on both diaspore and kaolinite decreased due to the reduced density of Al-active sites on the minerals surfaces. The changes of collector adsorption capacity and floatability of diaspore were very small while those of kaolinite were significantly increased. These changes were caused by decreasing the density of Al-active sites (covered by HMP and thereby preventing DAH adsorption) on both diaspore and kaolinite and increasing the density of Si-active sites of kaolinite (not covered by HMP and thereby facilitating DAH adsorption). The results clearly indicated that the acid treatment was shown to be conducive to changing the active Al- and Si-sites on diaspore and kaolinite and thereby improving their flotation separation.