In this study, response surface methodology (RSM) was used to optimize the experimental conditions in nitrate removal processes using 20 AEPTMS amine-functionalized MCM-41 as the adsorbent. The adsorbent was synthesized via co-condensation method and then characterized by using scanning electron microscope (SEM) and Fourier transform infrared spectroscopy (FTIR). Subsequently, total 19 adsorption experiments with different experimental conditions generated by the Design of Experiments (DoE) software have been conducted. The experimental results were fitted well with the quadratic model suggested by the software and the R2 value obtained was 0.9935. It was found that the highest percentage removal of nitrate was 70 obtained at initial nitrate concentration of 0.25 mM, adsorbent dosage of 0.50 g and contact time of 1 h. On the other hand, the optimum nitrate removal of 56 was obtained at the optimum conditions suggested by the software, with the initial nitrate concentration of 0.25 mM, adsorbent dosage of 0.124 g, and contact time of 1 h. © 2016 The Authors.