In order to alleviate the membrane fouling, a short flow drinking water process coupled the continuous sand filtration (CSF) to ultrafiltration (UF) was developed to treat the micro-polluted surface water and the membrane fouling mechanism was further discussed. The results indicated that the CSF process significantly enhanced the removal of ammonia (NH4+-N), accounting to an average removal of more than 70%. Furthermore, the natural organic matters (NOM) were also efficiently removed, with CODMn, UV254 and DOC reduced by approximately 30%, 17% and 18%, respectively. After 2 months of operation, the biological activity developed gradually within the CSF, which sparked an efficient removal performance of Fe and Mn. Besides, three dimensional fluorescence parallel factor analysis (PARAFAC) was employed to trace and characterize membrane fouling and a significantly positive correlation between the fluorescent foulants and irreversible fouling was observed. In addition, further simulations indicated that cake layer formation should be responsible for the trans-membrane pressure (TMP) increase. In order to gain a deep insight to the membrane fouling, the composition of foulants in the chemical backwash water was characterized, and humic substances and metal ions (i.e. Fe, Mn, Ca and Mg) were the main components, which demonstrated that the irreversible membrane fouling should be related to the synergistic effects of inorganic ion precipitates and humic substances. Overall, coupling CSF to UF filtration can significantly enhance its removal performance and control the membrane fouling, which is expected to be a promising alternative based on the principle of aquatic ecosystems for the micro-polluted raw water.