Compared to the eutrophication of lakes and reservoirs, the mechanism of river algal blooms in a flowing water body are more complicated, and often lead to serious consequence in catchment scale. Due to the simultaneous impact of a variety of environmental pressures, the water ecosystem integrity state often shows a response characteristic of accumulation, complexity and time lag, therefore it is difficult to use conventional hydrodynamic and water quality models to scientifically characterize and analyze. The lower Hanjiang River (HR) is an important influence area of the middle route of the South-to-North Water Diversion Project (SNWDP) in China, continuous river blooms issue has become a major national concern. In this study, a time-lag analysis approach was developed to identify the causes of algal blooms formation and the time-lag response law in the lower HR, including principal component analysis (PCA), grey relation analysis (GRA), and Almon Distributed Lag Model. Results found that, the hydrological regime (ΔH) contributes the most to the river bloom, especially due to the flow hindrance of the Yangtze River (YR) and the water project upstream. It is also found that the algal bloom outbreak in the lower HR is not an immediate response to the driving factors. It has a time lag of about 1 period (10 days) in the response with antecedent driving factors. Finally, we discussed the influence and its responding mechanism of ΔH on the growth of phytoplankton. The research can provide early warning for the prevention and control of algal blooms in the large river system.