In 2020, a sudden COVID-19 pandemic unprecedentedly weakened anthropogenic activities and as results minified the pollution discharge to aquatic environment. In this study, the impacts of the COVID-19 pandemic on aquatic environment of the southern Jiangsu (SJ) segment of Beijing-Hangzhou Grand Canal (SJ-BHGC) were explored. Fluorescent component similarity and high-performance size exclusion chromatography analyses indicated that the textile printing and dyeing wastewater might be one of the main pollution sources in SJ-BHGC. The water quality parameters and intensities of fluorescent components (WT-C1(20) and WT-C2(20)) decreased to low level due to the collective shutdown of all industries in SJ region during the Spring Festival holiday and the outbreak of the domestic COVID-19 pandemic in China (January 24th to late February, 2020). Then, they presented a gradual upward trend after the domestic epidemic was under control. In mid-March, the outbreak of the international COVID-19 pandemic hit the garment export trade of China and consequently inhibited the production activities of textile printing and dyeing industry (TPDI) in SJ region. After peaking on March 26th, the intensities of WT-C1(20) and WT-C2(20) decreased again with changed intensity ratio until April 12th. During the study period (135 days), correlation analysis revealed that WT-C1 and WT-C2 possessed homology and their fluorescence intensities were highly positively correlated with conductivity and COD_Mn. With fluorescence fingerprint (FF) technique, this study not only excavated the characteristics and pollution causes of water body in SJ-BHGC, but also provided novel insights into impacts of the COVID-19 pandemic on production activities of TPDI and aquatic environment of SJ-BHGC. The results of this study indicated that FF technique was an effective tool for precise supervision of water environment.