The effectiveness of combined nanofiltration and disinfection processes was studied by comparing the pre-disinfection and post-disinfection when in combination with nanofiltration. Four types of sulfonamide (sulfanilamide, sulfadiazine, sulfamethoxazole, and sulfadimethoxine) were chosen as substrates, with sodium hypochlorite as a disinfectant. A laboratory-scale nanofiltration system was used to conduct the following sets of experiment: (1) a pre-chlorination system, where the free active chlorine (FAC) was added to the membrane influent; and (2), a post-chlorination system, where the FAC was added to the membrane effluent. Overall, the pre-disinfection nanofiltration system showed higher sulfonamide removal efficiency compared to the post-chlorination nanofiltration system (>99.5% versus >89.5%). In the case of limited FAC ([FAC]0: [sulfonamide]0 ≤ 1), the removal efficiency for the post-chlorination nanofiltration system was higher, due to the prior nanofiltration process that could remove 12.5% to 80% of sulfonamide. The flux of the treated feed system was considerably higher than in the untreated feed system; however, the membrane was observed to be slightly damaged due to residual chlorine attack.