Removal of nitrate anion from aqueous solution stays one of the principal goals of much study concerning water treatment. Besides biological and membrane separation treatment, Anion exchange resin technique has been widely investigated and the most result was leading to an efficient elimination. In the proposed work an attempt to the utilization of commercial anion exchange membrane modified by adsorption of polyethyleneimine was investigated. Many conditions of modification of anion exchange resin surface were studied and the influence of the composition of treated solution was also examined. It is observed that the chloride/nitrate ratio has a direct consequence on the separation when modified resin by 2 day adsorption in 2 g/L polyethyleneimine solution at pH 10 was used. It is also concluded that increasing of the contact time between resin and polyethyleneimine solution lead to the decreasing of a separation between Cl- and NO3-. Moreover, the conducted study was applied to a real solution provided from underground water in the Sahara at the southern region of Algeria. The separation has been studied in the presence and in the absence of a commercial pesticide commonly used in the region. Obtained result showed that the more concentration of chloride anion the more influence of the pesticide on the fixation process.