The Three Gorges Project (TGP) has received many criticisms about its potential effects on the changes in the downstream ecosystems. Poyang Lake is the largest body of water downstream of the TGP, and it is not immune to these changes. TRMM and GRACE data were introduced in this study to estimate river-lake water exchange, from which the hydrological responses of Poyang Lake could be identified. A significant decreasing trend of the runoff coefficient has been observed since 2003, resulting in 6.02 km3 more water discharge from the lake into the Yangtze River than under normal conditions. No significant interannual changes occurred in the water level or local precipitation, and GRACE observations revealed that groundwater discharge appeared to be the most likely compensation for the water loss. A novel approach, namely, the groundwater abnormality index (GAI), was developed to depict the water exchange using GRACE and surface water observations. Lower than normal GAIs were found between 2003 and 2005, reaching a minimum of −29.26 in October 2003, corresponding to ten times of the mean GAI during 2006–2012, clearly indicating a significant water exchange in Poyang Lake Basin from groundwater to surface water after the TGP impoundment.