In this study, a purified diatomite (PD) with a concentration of diatom frustules more than 92% SiO2 was utilized to synthesize a composite of MCM-41 silica under hydrothermal conditions. The as-synthesized PD/MCM-41 composite was characterized and tested as an adsorbent for the removal of Cr(VI) and Mn(VII) ions from aqueous solution. Results of X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier-transform infrared spectroscopy (FTIR) revealed that the diatom frustules of the PD were coated with MCM-41 mesoporous silica. Experimental isotherms of Cr(VI) and Mn(VII) adsorption were fitted to classical and advanced statistical physics models at 25°C–55°C and pH 3. The Langmuir model estimated monolayer adsorption capacities ranging from 144.1 to 162.2 mg/g for Cr(VI) and 166.2 to 177.0 mg/g for Mn(VII), which improved with increasing the solution temperature. Steric and energetic parameters obtained from a monolayer adsorption model with one adsorption site was utilized to explain the adsorption mechanism at a microscopic level. The number of Cr(VI) and Mn(VII) ions adsorbed on PD/MCM-41 active site (n) were 1.25–1.27 for Cr(VI) and 1.27–1.32 for Mn(VII), thus suggesting multi-interaction mechanisms. The density of PD/MCM-41 active sites (DM) was a key parameter to explain the adsorption of these heavy metals. The adsorbed quantities were maximum at 55°C, thus obtaining 102.8 and 110.7 mg/g for Cr(VI) and Mn(VII), respectively. Cr(VI) and Mn(VII) adsorption energies ranged from 18.48 to 26.70 kJ/mol and corresponded to an endothermic adsorption with physical forces. Entropy, free enthalpy, and internal energy associated to the adsorption of Cr(VI) and Mn(VII) ions were calculated, thus indicating that the removal of these pollutants was spontaneous. Overall, this article offers new interpretations for the Cr(VI) and Mn(VII) adsorption mechanisms on PD/MCM-41 composite, which are relevant to contribute to the development of effective water treatment processes.