The hydrophobicity of dissolved organic matter (DOM) affects various aspects of its environmental impacts in terms of water quality, sorption behaviors, interactions with other pollutants, and water treatment efficiency. In this study, source tracking of river DOM was conducted separately for hydrophobic acid (HoA-DOM) and hydrophilic (Hi-DOM) fractions using end-member mixing analysis (EMMA) in an agricultural watershed during a storm event. EMMA with optical indices of bulk DOM revealed larger contributions of soil (24 %), compost (28 %), and wastewater effluent (23 %) to riverine DOM under high versus low flow conditions. Molecular level analysis of bulk DOM revealed more dynamic features, showing an abundance of CHO and CHOS formulae in riverine DOM under high- and low flow conditions. CHO formulae originated from soil (78 %) and leaves (75 %) and contributed to the increasing CHO abundance during the storm event, whereas CHOS formulae likely originated from compost (48 %) and wastewater effluent (41 %). The characterization of bulk DOM at the molecular level demonstrated that soil and leaves are the dominant contributors for the high-flow samples. However, in contrast to the results of bulk DOM analysis, EMMA with HoA-DOM and Hi-DOM revealed major contributions from manure (37 %) and leaf DOM (48 %) during storm events, respectively. The results of this study highlight the importance of individual source tracking of HoA-DOM and Hi-DOM for the proper evaluation of the ultimate roles of DOM in affecting river water quality and for a better understanding of DOM dynamics and transformation in natural and engineered systems. Display omitted •Source tracking was separately conducted for HoA- and Hi-DOM during a storm event.•Major sources were different between the HoA- and Hi-DOM in agricultural watershed.•Leaves were the major source contributor to Hi-DOM, whereas manure was to HoA-DOM.