Three-dimensional fluorescence spectroscopy is an emerging sensitive technology to detect organic pollution in water bodies. Based on this technique, a research group from Tsinghua University developed a novel instrument as a tool of pollution early-warning and pollution source identification, it has been put into use in A city in South China, for aqueous fingerprint monitoring and pollution sources identification under abnormal conditions. As a new monitoring method, it broke the limitation that traditional water quality monitoring technology could not provide directivity information of pollution source, and could detect abnormity of water quality quickly and identify pollution source accurately. In this paper, the process to identify pollution source during an abnormity incident of water quality in S River captured by the instrument was studied. When the instrument captured unidentified aqueous fingerprints during on-line monitoring, pollution intrusion process was inferred based on the variation of aqueous fingerprint figure and peak intensity. Then the pollution source identification was achieved by comparing the fingerprints between the polluted water body and possible pollution sources by the instrument. The source identification was verified with the changes of other water quality parameters such as pH, aniline, TOC and TN. The results showed that this early-warning and pollution source identification technique can quickly detect and release warning of abnormity of water quality and identify pollution sources accurately via monitoring aqueous fingerprints. The abnormity incident studied in this paper might be caused by dumping raw materials by a chemical plant located in upstream of the river.