The structure and size characterization of organic matter (OM) using flow field-flow fractionation (FFFF) is interesting due to the numerous interactions of OM in aquatic systems and water treatment processes. The estimation of hydrodynamic and electrostatic forces involved in the fractionation of OM over different molecular weight cut-off (MWCO) membranes is vital for a better understanding of the FFFF process. This work aims to understand the membrane-OM interactive forces with respect to membrane MWCO, solute molecular weight, flow rates, solution pH and ionic strength. Polystyrene sulfonate sodium salt (PSS) of molecular weights 10, 30 and 65 kDa were used as model organic solutes for fractionation over ultrafiltration (UF) membranes of MWCO 1–30 kDa. Maximum fractionation of PSS was achieved by using a tight membrane of 1 kDa MWCO at the conditions of high permeate flow rate (1.5–2.0 mL·min−1), low concentrate flow rate (0.2–0.3 mL·min−1) and low ionic strength (10 mM). The better fractionation corresponds to high permeate drag force and low concentrate drag force. A low membrane-solute DLVO interaction is favourable for the retention of a small solute. This study illustrated that FFFF characteristics can be analyzed based on membrane-solute interactive forces controlled by selected flow, size and charge parameters.