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To unravel fouling and defouling mechanisms of protein, saccharides and natural organic matters (NOM) on polymeric membrane during filtration, this study investigated filtration characteristics on polyvinyl chloride (PVC) ultrafiltration membranes with bovine serum albumin, dextran, humic acid as model foulants. Membrane fouling and defouling performances were analyzed through monitoring the flux decline during filtration and flux recovery during physical backwash. Physico-chemical properties (e.g., hydrophobicity and surface charge) of PVC membrane and foulants were characterized, which were used in the extended Derjaguin–Landau–Verwey–Overbeek (EDLVO) theory to calculate the interaction energies between membrane foulant and foulant-foulant. The results showed that at the later filtration stages the fouling rate was strongly correlated with the deposition rate, which was determined by the interaction energy profile calculated by EDLVO. Moreover, the adhesion forces of membrane–foulant and foulant–foulant were further measured by atomic force microscopy (AFM) with modified colloidal probes. A positive correlation (R2 =0.845) between particle detachment rate (determined by adhesion force) and defouling rate was developed for BSA and HA foulants that led to cake layer formation. By contrast, dextran defouling rate was off this correlation as dextran partially clogged membrane pores due to its smaller size.