The content of organic matter in ground environmental waters is an important indicator of the degree of organic pollution in waters. In order to understand the organic pollution and water quality in Yangtze River and Qingyi River in Wuhu section, inspecting the surrounding environment conditions and taking representative water samples along Yangtze River and Qingyi River in Wuhu section were done in this study. Total organic carbon content in water samples was determined by high temperature combustion - non-dispersive infrared absorption method. Based on these, the changes of TOC content and their impact factors in waters along Yangtze River and Qingyi River in Wuhu section was studied in this paper. The results showed that both waters along Yangtze River Water and Qingyi River in Wuhu section have a high level of TOC content, and the average value of TOC content in waters (except for some special sampling points) is 22.2±4.1 mg/L and 22.6±2.7 mg/L, respectively. The TOC content of some individual water samples from Qingyi River has exceeded the value of 40mg/L. According to the national standard, the TOC content in waters of both Yangtze River and Qingyi River has exceeded the value of the Ⅰ standard, and TOC content of some sampling water from Qingyi River has exceeded theⅡ standard.