• The catchment inflow of the Poyang Lake (CIPL) dominates variations in the Poyang Lake’s outflow ( Q h ). • The Yangtze River forcing dominates variations in water level at the conjunction of river and lake ( Z h ). • The sensitive coefficients of seasonal Q h to the CIPL and that of Z h to the Yangtze River forcing are evenly 0.63 and 0.41, respectively. • The daily backflow with discharge exceeding and below 3000 m 3 /s is mainly influenced by the CIPL and the Yangtze River forcing, respectively. The driving factors of water exchange in the Yangtze–Poyang river–lake system (YPRLS) which is vital to the water resource management of YPRLS still remain unclear. In this study, the impacts of three major factors on the water exchange in the YPRLS from 1989 to 2016 were distinguished. Our results revealed that the catchment inflow into Poyang Lake (CIPL) dominates the variations in Q h (the discharge of Poyang Lake’s outflow), contributing nearly 100 % of the annual variation and evenly 120 % of the seasonal variations. The forcing of the Yangtze River, including the effect of operation of the Three Gorges Dam (TGD) and effects of other Yangtze-related factors in addition to it, stably explains approximately over 76 % of the annual and seasonal variations in Z h (water level at the junction of the river and lake). The sensitivity coefficient of the seasonal Q h to the CIPL and that of the seasonal Z h to the forcing of the Yangtze River, varying with the seasons, are 0.63 and 0.41, respectively. Furthermore, the CIPL-induced and the Yangtze-induced frequency of the backflow from the river to the lake (BRL) is 26 times and 7 times, respectively. Specifically, the frequency of BRL events with backflow discharge of <3000 m 3 /s and >3000 m 3 /s is mainly affected by the CIPL and the forcing of the Yangtze River, respectively. The variations in the seasonal Z h are speculated to be influenced by the water regime and the stage–discharge relationships, which may explain the stable dominate of the forcing of the Yangtze River on the seasonal Z h , and may affect the timing of autumn drought in the Poyang Lake. Our results may help to capture the main causes of complex hydrological changes in the YPRLS.