Calcium ions, magnesium ions, and silicate were the main reasons for the high silting density index (SDI) of natural waters. Therefore, they posed serious membrane fouling problems in the nanofiltration (NF) system, which restricted the wide application of this excellent drinking water treatment technology. In this study, the sand filtration and the micro-flocculation/sand filtration hybrid process were investigated as the pretreatment process of NF for SDI reduction. Compared with the sand filtration, the hybrid process of micro-flocculation/sand filtration was more effective for SDI reduction. When polyaluminium chloride (PAC) was used as the flocculant at a dose of 10 mg/L and the filtration rate of the sand filter was controlled at 10 m/h, the SDI value in the effluent of the pretreatment process maintained below 3. As a result, the subsequent NF system stably ran for one year. 68% CODMn was removal by NF. The membrane fouling during the operation was quite slight as the transmembrane pressure (TMP) increased by 17% after one-year use. Chemical cleaning with sodium tripolyphosphate (2%) and sodium dodecyl benzene sulfonate (0.25%) at 6 months interval could effectively recover the flux loss of the NF membrane.