Abstract This work investigates the effects of flow rate (5–15 Bed Volumes/h), particle size (0.8–1.7 mm), concentration (0.005–0.02 N) and Na +-enrichment of natural clinoptilolite on the removal efficiency of Pb 2+, Cu 2+, Fe 3+ and Cr 3+ in aqueous solutions. Ion exchange is performed in an upflow fixed bed reactor. The removal efficiency is increased with decreasing flow rate, particle size and concentration and is improved by a factor of 2–10, depending on the specific metal. The modification of the natural sample is favorable, leading to an increase of removal efficiency by 32–100%. For the experimental conditions examined, removal efficiency order is the following: Pb 2+>Cr 3+>Fe 3+≥Cu 2+. Finally, the operation is influenced by the studied parameters, following the order: concentration>volumetric flow rate> particle size > modification of the material.