Accelerated export of nitrogen-containing dissolved organic matter (DOM) or dissolved organic nitrogen (DON) to streams and rivers from agricultural watersheds has been reported worldwide. However, few studies have examined the dynamics of DOM molecular composition with the attention paid to the relative contributions of DON from various sources altered with flow conditions. In this study, end-member mixing analysis (EMMA) was conducted with the optical properties of DOM to quantify the relative contributions of several major organic matter sources (litter, reed, field soil, and manure) in two rivers of a small agricultural watershed. DOC and DON concentration increased during the storm events with an input of allochthonous DOM as indicated by an increase in specific ultraviolet absorbance at 254 nm (SUVA254) and a decrease in biological index (BIX), fluorescence index (FI), and protein-like component (%C3) at high discharge. EMMA results based on a Bayesian mixing model using stable isotope analysis in R (SIAR) were more accurate in source tracking than those using the traditional IsoSource program. Manure (>30%) and field soil (also termed as “manure-impacted field soil”) (>23%) end-members revealed their predominant contributions to the riverine DOM in SIAR model, which was enhanced during the storm event (up to 56% and 38%, respectively). The molecular composition of the riverine DOM exhibited a distinct footprint from the manure and manure-impacted field soil, with a larger number of CHON formulas and abundant polyphenols and condensed aromatics in peak flow samples in the studied rivers. The riverine DOM during peak flow contained many unique molecular formulas in both rivers (4980 and 2082) of which >60% originated from manure and manure-impacted field soil. Combining the EMMA with DOM molecular composition clearly demonstrated the effect of manure fertilizer on the riverine DOM of the watershed with intensive agriculture. This study provides insights into the source tracking and regulation of DON leaching from anthropogenically altered river systems worldwide.