<p>The Qingcaosha Reservoir has been experiencing eutrophication, which has resulted in algal blooms. This led to heightened levels of chlorination by-products, posing a significant concern. This study evaluated the trend of trihalomethanes (THMs) in Shanghai’s drinking water before and after the reservoir’s algae monitoring program and associated health risks. The results indicated that the concentrations of total THMs, trichloromethane (CHCl₃), monochlorodibromomethane (CHBr₂Cl), dichloromonobromomethane (CHBrCl₂), and tribromomethane (CHBr₃) were below the limits stipulated by China’s standards for drinking water quality (GB 5749–2022). Total THMs concentrations also remained below the WHO and EU limits (100&#xa0;µg/L) and the US EPA limit (80&#xa0;µg/L). Following the intervention from 2014 to 2020, there was a significant reduction in total THMs, CHCl₃, and CHBr₂Cl in the finished water (<i>P</i> &lt; 0.05), whereas CHBr₃ and CHBrCl₂ concentrations remained unchanged. By 2020, the carcinogenic risk of the total THMs was higher than 1 × 10⁻⁶ but lower than 1 × 10⁻⁴, consistent with acceptable levels recommended by the EPA, although the non-carcinogenic risk, indicated by the hazard quotient (HQ), was below 1. This study demonstrates that the algae monitoring and control program at Qingcaosha Reservoir during peak water supply periods has effectively lowered chlorinated disinfection by-product levels in the finished water of a water treatment plant in Shanghai since 2014, significantly decreasing health risks. Future efforts should focus on strengthening eutrophication and algal bloom management in water sources and improving water treatment processes to further decrease disinfection by-product content.</p>