Soluble microbial products (SMPs) discharged into rivers from sewage treatment plants may increase the health risk for downstream drinking water by acting as a precursor of DBPs. Biotransformation or biodegradation could alter the characteristics of SMPs and affect the subsequent formation of DBPs. This study observed the relative contribution of chemical fractions in SMPs and explored the biodegradation of each fraction and their effect on disinfection by-products (DBPs) formation in surface water. The hydrophilic acid (HPIA) and hydrophobic acid (HPOA) constituted the major portion of the SMPs, which were dominated by fulvic acid and humic acids. The transphilic acid (TPIA) and hydrophobic bases (HPOB) were relatively minor but it contained a relative substantial portion of protein-like materials in SMPs. TPIA and HPOB produced insignificant amounts of DBP corresponding to 13% and 14% in the original samples, but they were collectively responsible for 50% of the DBPs yield. Much larger amounts of hydrophobic fractions were utilized than hydrophilic fractions after biodegradation. The increase in SUVA values indicating aromatic structures, except for HPOA fraction, was observed after biodegradation. The protein-like materials in both the HPOA and HPIA fractions and polycarboxylate-type humic acid in the HPIA fraction decreased but the enrichment of HPOA (MW > 100 kDa) and TPIA (MW < 1 kDa) was observed after biodegradation. The production of = C–H in HPIA fraction and the appearance of double peak at 1100 cm−1 in TPIA and HPOB fractions occurred after biodegradation. In overall level, microorganisms effectively utilized DBP precursors from HPIA, HPOA and HPOB fractions but increased the DBPs precursors from the TPIA fraction. TPIA and HPOB fractions had higher DBP yield with chlorine but the DBPs yield of HPIA and HPOA changed little after biodegradation.