With development of society and population growth, conflict between water supply and demand becomes increasingly sharp and low water issue attracts growing attention from the public. In this paper, a root cause analysis (RCA) is used as a tool to examine the major factors of low flow alteration systematically, and these factors and their relationship are clearly shown using a causality tree diagram. In a case study of the Dong River basin, low flow series at its hydrological stations were analyzed. Results show change points that occurred in the low flow series at four stations on the river mainstream and and the variations had obvious mutual correlation. A causality tree diagram of the variations was constructed using the data of flow, rainfall, evaporation, and features of the reservoirs in this basin. This study comes to the following conclusions: Influence of climate change on runoff variations was insignificant in the East River case; the major influences in this basin were originated from frequent human activities; the variations in low flow series were caused by the runoff regulation at the Fengshuba reservoir and Xinfengjiang reservoir.