All surface and ground waters contain natural organic matter (NOM). NOM is a complex mixture of various organic molecules mainly originating from aquatic organisms, soil and terrestrial vegetation. When chlorine is applied to drinking water processes, it reacts with NOM and forms various types of chlorinated disinfection by-products (DBPs). These halogenated by-products are considered to be possible human carcinogens. Trihalomethanes (THMs) and haloacetic acids (HAAs) are the most widely known DBPs. Through the different reaction reactivity of the NOM components with disinfectants, the isolation and fractionation of NOM into more homogenous components is a better way to determine the DBP formation potential in the waters. Characterization of the NOM is also important for the selection of drinking water treatment processes because the US Drinking Water Regulations force water utilities to further increase DBP precursor removal by removing DOC to below 2 mg/L. In this study, using Omerli (OM) and Buyukcekmece (BC) surface water samples which were obtained over a 1-year period, the NOM content was isolated and chemically fractionated by means of XAD resins. In addition, each fraction was chlorinated separately and THMs and HAAs formation potential (THMFP and HAAFP) was investigated. The results indicated that both water chemical phases changed on a seasonal basis. This affects the DBPFP of waters. Hydrophobic (HPO) fraction was detected to be the highest percentage of the DOM in both OM and BC. But in terms of the DBPFP dominant phase, this changes seasonally. These results indicated that OM and BC surface waters include THM and HAA precursors and variations of these fractions are also effective for treatment process selection and attaining consistency in drinking water quality.