This study presents data on the water quality of the Guarani Aquifer based on samples collected from distinct groundwater wells in the western region of Santa Catarina State, Brazil. Among the analyses performed, the results indicated the need for treatment to ensure suitability for human consumption, particularly concerning Fe³⁺ and Mn²⁺ ions. Accordingly, natural (NCLIN) and activated clinoptilolite (ACLIN) zeolites were evaluated for ion removal from synthetic aqueous solutions through adsorption. NCLIN demonstrated excellent performance in adsorbing Fe³⁺ and Mn²⁺ ions, achieving removal efficiencies of over 98% and 95%, respectively, at a controlled pH of 6.0 (NCLIN) or 4.0 (ACLIN). A non-linear approach to modeling adsorption kinetics indicated that the pseudo-second-order model best represented the experimental data. This finding suggests that the interaction between the adsorbent and Fe³⁺ and Mn²⁺ ions occur through electron sharing and chemisorption. Equilibrium modeling analysis revealed that adsorption on NCLIN occurred in a monolayer, whereas adsorption on ACLIN followed a multilayer pattern. This behavior is attributed to the activation process with H₂SO₄, which led to dealumination and the formation of HSO₃⁻ groups on the adsorbent surface.