Excessive use of pesticides and therefore the spread of pesticides in the environment with destructive effects on human and animal health is a very great problem in the world. In this study, the removal of three samples of organochlorine pesticides including aldrin, lindane, and endosulfan was investigated using nanofiltration membranes modified with NH2-MWCNTs. The properties of the prepared membranes were investigated by scanning electron microscopy (SEM), contact angle, water content, porosity, and mechanical strength. The performance of the membranes was evaluated by analysis of the rejection and flux of pesticide solutions at different pH. The addition of NH2-MWCNTs to the polymer matrix significantly improved the hydrophilic properties of the membranes and reduced the contact angle. Membrane flux was also improved by increasing the concentration of carbon nanotubes to 0.2 wt%. The highest flux at pH 10 is related to lindane pesticide. The modified membrane with 0.5 wt% functionalized carbon nanotubes showed a 98% rejection for endosulfan at neutral pH compared to the pure membrane. In the pH range experiment, lindane rejection was lower than of other pesticides. The steric hindrance due to the structure and molecular size of pesticides and interaction with membrane surface was very important in membrane efficiency. The M3 membrane with 0.3 wt% NH2-MWCNTs revealed high antifouling performance.