In the present study, the impact of RO polyamide layer by long-term chemical exposure was evaluated. Basic cleaning chemicals such as NaOH increased the pure water flux and salt passage of RO membrane up to 1.6 times and 2 times, respectively. In contrast, membranes exposed to acidic chemicals such as HCl have experienced no discernible change of permeability, which indicated that basic chemicals caused the more serious damage to RO polymeric layers. However, XPS analysis showed that both membranes were experienced significant damages on cross-linking of polyamide structures. It can be concluded that basic cleaning chemicals induced the enlarged pore structure due to electrostatic repulsion between damaged polymers, while acidic chemicals caused less performance deterioration by shrinkage of the polyamide structure.