Abstract To fight against the coronavirus infectious disease-2019 (COVID-19), chlorine-based disinfectants are extensively or even over used for water, surface and personal care decontamination. The risks of disinfection by-products (DBPs) have been alerted to cause serious secondary pollution; however, there is still lack of evidence. This study collected 110 water samples from nine lakes and two rivers in Wuhan during the COVID-19 pandemic and comprehensively analyzed the occurrence of eighteen DBPs. Trihalomethanes, halonitromethanes, halogen acetonitriles and nitrosamines had a high detection frequency and were 0.99-14.26, ND-4.62, ND-1.09 and 0.0414-0.0861 μg/L, respectively, all lower than the maximum contamination level (MCL) suggested by China and USA. Haloacetic acids were detected in all lakes and Yangtze River and ranged from 33.8 to 856.1 μg/L, much higher than the MCL. Haloacetic acids and halogen acetonitriles accounted for 74.2-95.1% of the total cytotoxicity (0.38-3.62×105); halonitromethanes (94.0-98.7%) contributed to the majority of genotoxicity (0.52-5.17×104). Dichloroacetic acid exhibited significant ecological risks to green algae in two lakes and Yangtze River (risk quotient >10), and all the other DBPs showed negligible risks (risk quotient <0.01) to fish, daphnid or green algae. Correlation and redundancy analysis identified strong correlations between total organic carbon, conductivity, NH3-N, turbidity and DBPs. DBP composition and the fluorescence indices of dissolved organic matters together categorized all lakes into two types. Type-I lakes contained all DBP categories, driven by total organic carbon and secondarily formed by residual active chlorine with natural organic matters; Type-II lakes and Yangtze River only had high levels of haloacetic acids and small amounts of trihalomethanes, explained by the primary formation of DBPs in sewage. Our findings for the first time uncovered the significant accumulation and risks of DBPs in lakes and rivers of Wuhan during the COVID-19, provided the evidence of secondary pollution from intensive disinfection activities with chlorine-based disinfectants, evaluated the potential the ecological risks of DBPs in Wuhan and along Yangtze River, and raised our re-consideration of disinfection strategy in the pandemics and post-COVID-19 era.