The impacts of membrane degradation due to chlorine attack on the rejection of inorganic salts and trace organic contaminants by nanofiltration (NF) and reverse osmosis (RO) membranes were investigated in this study. The rejection of trace contaminants was examined at environmentally relevant concentrations. Changes in the membrane surface morphology were observed as a result of chlorine exposure. A small increase in rejection was consistently observed with all four membranes selected in this study after being exposed to a low concentration of hypochlorite (100 ppm). In contrast, a higher concentration of hypochlorite (i.e., 2000 ppm) could be detrimental to the membrane separation capacity. Membranes with severe chlorine impact showed a considerable decrease in rejection over filtration time, possibly due to rearrangement of the polyamide chains under the influence of chlorine degradation and filtration pressure. The reported results indicate that loose NF membranes are more sensitive to chlorine exposure than RO membranes. The impact of hypochlorite exposure (both positive and negative) on rejection is dependent on the strength of the hypochlorite solution and is more significant for the neutral carbamazepine compound than the negatively charged sulfamethoxazole.