Three Gorges Reservoir (TGR) is one of the largest man-made lakes in the world. Since the impoundment in 2003, however, algal blooms have been often observed in the tributary embayments. To control the algal blooms, a thorough understanding of the hydrodynamics (e.g., flow regime, velocity gradient, and velocity magnitude and direction) in the tributary embayments is particularly important. Using a calibrated three-dimensional hydrodynamic model, we carried out a hydrodynamic analysis of a typical tributary embayment (i.e., Xiangxi Bay) with emphasis on the longitudinal patterns. The results show distinct longitudinal gradients of hydrodynamics in the study area, which can be generally characterized as four zones: riverine, intermediate, lacustrine, and mainstream influenced zones. Compared with the typical longitudinal zonation for a pure reservoir, there is an additional mainstream influenced zone near the mouth due to the strong effects of TGR mainstream. The blooms are prone to occur in the intermediate and lacustrine zones; however, the hydrodynamic conditions of riverine and mainstream influence zones are not propitious for the formation of algal blooms. This finding helps to diagnose the sensitive areas for algal bloom occurrence.