The East River in the Pearl River basin, China, plays a vital role in the water supply for mega-cities within and in the vicinity of the Pearl River Delta. Knowledge of statistical variability of streamflow is therefore important for water resources management in the basin. This study analyzed streamflow from four hydrological stations on the East River for a period of 1951–2009, using ensemble empirical mode decomposition (EEMD), continuous wavelet transform (CWT) technique, scanning t and F tests. Results indicated increasing/decreasing streamflow in the East River basin before/after the 1980s. After the early 1970s, the high/low flow components were decreasing/increasing. CWT-based analysis demonstrates a significant impact of water reservoirs on the periodicity of streamflow. Scanning t and F test indicates that significantly abrupt changes in streamflow are largely influenced by both water reservoirs construction and precipitation changes. Thus, changes of streamflow, which are reflected by variations of trend, periodicity and abrupt change, are due to both water reservoir construction and precipitation changes. Further, the changes of volume of streamflow in the East River are in good agreement with precipitation changes.