Rivers play an important role in the global water cycle, support biodiversity and ecological integrity. However, river flow and thermal regimes are heavily altered in dammed rivers. These impacts are being exacerbated and become more apparent in rivers fragmented by multiple dams. Recent studies mainly focused on evaluating the cumulative impact of cascade reservoirs on flow or thermal regimes, but the role of upstream reservoirs in shaping the hydrology and hydrodynamics of downstream reservoirs remains poorly understood. To improve the understanding of the hydrodynamics in cascade reservoirs, long-term observational data are used in combination with numerical modeling to investigate the changes in flow and thermal regime in three cascade reservoirs at the upper reach of the Yangtze River. The three studied reservoirs are Xiluodu (XLD), Xiangjiaba (XJB) and Three Gorges Reservoir (TGR). In addition, the effects of single reservoir operation (at seasonal/daily time scale) on hydrodynamics are examined in a large tributary of TGR. The results show that the inflow of TGR has been substantially altered by the two upstream reservoirs with a higher discharge in spring and winter and a reduced peak flow in summer. XJB had no obvious contribution to the variations in inflow of TGR. The seasonal water temperature of TGR was also widely affected by the upstream two reservoirs, i.e., an increase in winter and decrease in spring, associated with a delay in water temperature rise and fall. These effects will probably be intensified in the coming years due to the construction of new reservoirs. The study also underlines the importance of reservoir operation in shaping the hydrodynamics of TGR. The seasonal dynamics of density currents in a tributary bay of TGR are closely related to seasonal reservoir operations. In addition, high-frequency water level fluctuations and flow velocity variations were observed in response to periodic tributary bay oscillations, which are driven by the diurnal discharge variations caused by the operation of TGR. As another consequence of operation of cascade reservoirs, the changes in TGR inflow weakened spring thermal stratification and caused warming in spring, autumn and winter. In response to this change, the intrusions from TGR occurred more frequently as overflow and earlier in spring, which caused a sharp reduction in biomass and frequency of phytoplankton blooms in tributary bays of TGR. This study suggests that high-frequency bay oscillations can potentially be used as an efficient management strategy for controlling algal blooms, which can be included in future multi-objective ecological conservation strategies.