Rainstorm events can flush large amounts of terrestrial organic-rich material into lakes that are used for drinking water. To date, few studies have been carried out to investigate how rainstorm events change the molecular composition, bio-lability, and flux of upstream-imported dissolved organic matter (DOM), which can impact the odor and taste of drinking water as well as the efficiency of wastewater treatment. We undertook high-frequency buoy monitoring and point sample collection (n = 495), during high, moderate, and low inflow discharge, in Lake Qiandao, a key drinking water source for about 10 million people. Data from two online fluorescent DOM sensors deployed and field samples collected at the river site, Jiekou, and the lake site, Xiaojinshan, showed that rainstorm events increased the specific UV absorbance (SUVA254), humification index (HIX), humic-like components (C1-C2), and FT-ICR MS derived condensed aromatic and polyphenolic compounds (p < 0.001) and decreased the spectral slope of DOM (S275–295), spectral slope ratio (SR), biological index (BIX), and highly bio-degradable peptide-like and aliphatic substances (p < 0.001). Our results suggest that rainstorm events enhanced the export to the lake of colored, hydrophobic, and aromatic DOM. Upstream-derived dissolved organic carbon (DOC) concentrations decreased (p < 0.001), while DOC bio-availability (BDOC) increased only slightly (p < 0.05) during rainstorm events. The loss rate of DOC in Lake Qiandao is 0.82 × 104 t C yr−1, of which 0.30 × 104 t C yr−1 is highly bio-labile, and higher occurrences of both ≥ 25 mm d − 1 and ≥ 50 mm d − 1 rainfall events are anticipated by linear fittings for this region in the future. The application of in situ fluorescence sensors provides an early warning of DOC surge incidents caused by rainstorm events and may be useful in advising drinking water treatment plant managers of changes in raw water DOM quality and treatability.