Seasonal fluctuations of phytoplankton have often been regarded as one of the important cyclic events in aquatic ecosystems, and have even been emphasized as an important sign of regional climatic variability in limnology. However, few attempts have been made to examine synchrony for phytoplankton fluctuations among different habitats in a single reservoir system. The present study employed Spearman rank correlation analysis and the Mantel test to assess levels of synchrony for phytoplankton abundance and taxonomic composition from reservoir mainstream to a tributary bay (Xiangxi Bay) in a giant dendritic reservoir, China (Three Gorges Reservoir, TGR). At the selected scale, asynchronous patterns of phytoplankton were found when looking at total abundance and taxonomic composition, suggesting that regional drivers were not strong enough to synchronize phytoplankton fluctuations, and local regulators were predominant. As a riverine system, the mainstream of TGR had high levels of algal synchrony, while asynchronous patterns of phytoplankton were detected within Xiangxi Bay, which is characterized as a lacustrine system. The present study further confirmed that external hydrological disturbances strongly homogenize habitat conditions and synchronize phytoplankton fluctuations within the mainstream, while spatial divergence of phytoplankton succession depend on local habitat conditions within Xiangxi Bay. Moreover, low synchrony of phytoplankton between the mainstream and Xiangxi Bay is probably caused by spatial divergence of phytoplankton succession within Xiangxi Bay and the lack of succession in the rapidly flushed mainstream. Independently of these mechanisms possibly explaining phytoplankton fluctuations, the present study has also an applied perspective to the improvement of a long-term observation program in which phytoplankton trends at the mainstream scale could be compiled from the data set in a single site, while a set of sampling sites should be required at the Xiangxi Bay scale.