The distribution characteristics of the biological communities in the flood plain areas of Lake Poyang are greatly influenced by the hydrological connectivity between a region and the main lake. Due to the water level fluctuations, the hydrological connectivity of the eastern bay of Lake Poyang is sensitive to the water level of the main lake. Taking the eastern bay of Lake Poyang as an example, this study analyzed the water level fluctuations in the main lake as well as its influences. The hydrological connectivity between the eastern bay and the main lake was quantitatively characterized from the aspects of connectivity days and occurrence time. Furthermore, the changes of hydrological connectivity and its potential impacts on the habitats of wetland plants and migratory birds were discussed. The results showed that when the water level was 13-16 m asl, there was a good hydrological connectivity between the eastern bay and the main lake, during which the suitable habitat area for the survival of wetland plants was the largest. The water level of the main lake has generally decreased since 2003, and the durations of low water levels have been prolonged. According to the results of IHA/RVA analysis, the water levels in the main lake had changed to a moderate extent, with an overall change degree of 40.2%. The hydrological connectivity between the eastern bay and the main lake has changed significantly, with annual connection days reduced by 46.2 days, and the variation is 15.9%. The occurrence time of non-connection period is about one month earlier, and the yearly time span is longer. The decreased hydrological connectivity caused the average water level of the eastern bay to drop by 0.6 m from March to October, with a decrease of about 1 m from September to October, while the water surface area corresponding to the suitable water depth for Carex sp. and Vallisneria natans increased in most months, especially from September to October (more than 40%), but the area of submerged macrophytes decreased and the biomass of hygrophytes increased. The weakening of hydrological connectivity led to the early emergence of the beaches, the transfer of hygrophytes such as Carex cinerascens to the center of the saucer-shaped lake, the decrease of the upper limit of submerged macrophytes such as Vallisneria natans by about 1 m, and the migration of migratory birds to the center of the lake or other shoals. In order to effectively protect the Lake Poyang wetland ecosystem, it is recommended that more attention should be payed to the regulating and control roles of the Three Gorges Dam on the Changjiang River in mitigating the impacts of changes in hydrological connectivity on wetland plants growth and migratory bird habitats in the flood areas of the lake.