Rivers serve as one of the main sources of water supply. Human activities, salts in the soil and rocks and urban runoffs, as well as air contaminants, lead to contamination of river water. In this research, Gamasiab river, which is the upstream of Karkheh river, was selected as a case study. Sixteen stations were selected along this river to determine the sulfate content of water samples. Samples were taken from these stations according to the guidelines (ISO 5667-5, 1991). The samples were then transferred to laboratory and were filtered using nanoparticles of natural clinoptilolite. The X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM) andFourier-Transform Infrared Spectroscopy (FTIR) images were taken to determine the properties of the adsorbents. The images indicated that the selected methods for preparation of the nanoparticles were correctly implemented. After examining the filtered samples, the adsorption efficiency was 95% for clinoptilolite. Whatman filter paper 42 was used for desorption of the natural nano-clinoptilolite. Adsorption isotherm of the natural clinoptilolite was Freundlich with a determination coefficient of R2=0.918. By using Design Expert software and assumption of two pH factors and adsorbent to contaminant ratios (D/C), optimum adsorption points were found and theoretical adsorption values were calculated as well. Results showed that the optimum adsorption points for clinoptilolite were pH = 9.51 (mg)adsorbent/(mg/l)initial and D/C=18.91(mg)adsorbent/(mg/l) initial. Comparison of the adsorbent function indicated that clinoptilolite had good performance in removal of sulfate ion from river water samples.