Polytetrafluoroethylene (PTFE) membrane has high resistance to chlorine, which is a great advantages in chemical cleaning to recover water flux during membrane processes in drinking water systems. A humic kaolin water with approximately 4 mg/L of DOC and 10 NTU of turbidity was prepared as a feed water. Coagulation pretreatment with or without settling was applied. The coagulation with settling showed the greatest water production. The reduced flux was effectively recovered by NaOCl cleaning, i.e., 21% recovery by 50 mg/L of NaOCl cleaning and 49% recovery by 500 mg/L NaOCl cleaning. The images of SEM and AFM analyses were corresponded to the water flux variation. However, when the floc was accumulated on the membrane surfaces, the efficiency of NaOCl cleaning was substantially limited. In addition, dynamic contact angle became greater after cleaning, which indicates changes in characteristics of fouling layer such as surface hydrophobicity. Proper cleaning technologies during enhanced backwash using NaOCl would expand application of PTFE membranes in drinking water systems.