The sediment load in the Yangtze River downstream of the Three Gorges Dam (TGD) has substantially declined in recent decades. The decrease is more profound below the TGD, e.g., a 97% decrease at Yichang, compared with that at the delta apex, 1200 km downstream, e.g., a 75% decrease, implying along-river sediment recovery. Two large river-connected lakes, i.e., Dongting and Poyang Lakes, may play a role in the re-establishment of the river’s morphodynamic equilibrium, but a quantitative data-based understanding of this interaction is not yet available. In this work, we collected a series of field data to quantify the sediment gain and loss in the river-lake system in the middle-lower Yangtze River, and evaluate the lake’s response to the reduction in riverine sediment supply. We find that Dongting Lake and Poyang Lake shifted from net sedimentation to erosion in 2006 and 2000, and back to a sedimentation regime again after 2017 and 2018, respectively. Natural morphodynamic adaptation and sand mining play an important role in the regime changes in the Dongting Lake whereas sand mining dominates the abrupt changes in the Poyang Lake. The Dongting and Poyang Lake contributed maximum by 38% (2015) and 17% (2006) (respectively) to the sediment recovery in the erosion regime, whereas the riverbed erosion dominates the main sediment source. These changes in the relative contribution of sediment sources also indicates a response time of ~ 20 years in the lakes towards a new equilibrium state. It is noteworthy that the lakes’ buffer effects may be overestimated as the supplied sediment from the lakes is rather small compared to the significant dam trapping in the upstream basin and sediment source from downstream degradation. The results imply that river management and restoration should take into account of the river-lake interactions and feedback impact at decadal time scales.