Understanding the effects of chlorine exposure on polyamide (PA) based membranes is essential in membrane lifespan improvement. In this study, NF90 nanofiltration membrane was treated with sodium hypochlorite at different concentrations, pHs and durations. The changes in membrane elemental composition and bonding chemistry obtained from XPS and ATR-FTIR revealed the impacts of two competing mechanisms: N-chlorination and chlorination-promoted hydrolysis. More chlorine was incorporated into the PA matrix at pH <7, at which HOCl is dominant, while chlorine-promoted hydrolysis was more favorable at pH >7 with abundant hydroxyl groups. The membrane surface became more hydrophobic when chlorination was dominant, which in turn caused the water permeability of chlorinated membrane to decrease. Meanwhile, membrane became more hydrophilic and less cross-linked when hydrolysis effects were governing, which made the membrane more permeable for water. Rejection of charged solutes [NaCl, As(V)] improved in most chlorinating conditions due to increased charge density. However, when hydrolysis was severe (≥ 1000 ppm, pH 7 and 9), the enhanced charge repulsion effect could not compensate for the extensive amide bond cleavage, resulting in declined rejection. The lower rejection of neutral boric acid provided strong evidence of a less cross-linked separation layer.