To better understand the influence of heavy precipitation event on water supply security, the change of nutrients, dissolved organic matter (DOM) and their corresponding disinfection by-products (DBPs) generation in river were investigated through a heavy precipitation event. The results show that short-term sustained heavy precipitation causes additional load on the river. Significant temporal variations and increases in dissolved oxygen (DO), turbidity, dissolved organic carbon (DOC) and molecular weight of raw water were observed during the heavy precipitation, and dissolved organic nitrogen (DON) showed a remarkably decline with the continuation of precipitation. The molecular weight and aromaticity of DOM increased dramatically with the continuous superposition of precipitation and flow, and the proportion of hydrophobic fraction increased during the study period. Four different fluorescent components were identified, including humic-like (C1, C2 and C3), and protein-like fluorophore C4. Heavy precipitation events affected the mobilization of DOM, while the generation of DBPs increased by 4%–47% during the chlorination, and the elevated river level further increased the DBPs formation. In particular, the HOA fraction was the main contributor of DBPs (up to 70%). The risk of haloacetic acids (HAAs) generation caused by heavy rainfall was concentrated in the river runoff producing and regression periods for both hydrophobic and hydrophilic fractions of DOM. Humification index (HIX) was positively correlated with the yield level of TCM, DCAA, TCAA, and DCAN during chlorination. Chlorination disinfection of raw water during river runoff producing and regression period is likely to increase the haloacetonitriles formation potential (HANsFP), thus posing a vital threat to water supply safety, while chloramination disinfection may significantly relieve the threat. This study provides a theoretical basis for the direct/indirect link between short-term precipitation events and their impact on water quality.