In the present study, batch and fixed bed experiments were conducted in order to compare clinoptilolite and vermiculite for the removal of Mn²⁺, Zn²⁺, and Cr³⁺ from aqueous solutions under the same experimental conditions. Ion-exchange equilibrium is examined by use of batch equilibrium isotherms, distribution coefficients, and maximum exchange levels (MEL). Fixed bed experiments were conducted, and breakthrough curves and operational capacity were determined. Furthermore, diffusion coefficients were estimated by use of simplified fixed bed models. Concerning the comparison of the two minerals, in all experiments, for both batch (distribution coefficients and MEL) and fixed bed (breakthrough points and operating capacity (OC)), vermiculite showed better performance than clinoptilolite for all metals. Vermiculite selectivity series derived from batch distribution coefficients as well as in fixed beds is Cr³⁺ > Zn²⁺ > Mn²⁺ and is the same for clinoptilolite for liquid-phase equilibrium at relative concentration of X < 0.2. For more concentrated equilibrium solutions, the clinoptilolite selectivity changes for Cr³⁺ and remains the same for the other two metals, i.e. Zn²⁺ > Mn²⁺ > Cr³⁺. MEL are 14.4–26.9 mg/g and 34.2–43.6 mg/g for clinoptilolite and vermiculite, respectively, and OC is found to be 3.6–7.9 mg/g and 12.8–29.3 mg/g for clinoptilolite and vermiculite, respectively, 25–75% lower than MEL. The application of the simplified fixed bed model is successful for Zn in both minerals and Cr³⁺-vermiculite system. For Cr³⁺-clinoptilolite system, the model is not applicable due to the sigmoidal shape of the isotherm while for Mn, the model fails in low concentrations for both minerals, and it seems to approach experimental data only for X > 0.2–0.3. Solid-phase diffusion coefficients were estimated to be in the order of magnitude of 10⁻⁸ cm²/s for clinoptilolite and 10⁻⁹ cm²/s for vermiculite.