Abstract: As important components of the Changjiang River water system, Dongting Lake and Poyang Lake play a crucial role in flood regulation, water supply security, ecological maintenance, and regional development. Under the dual influence of natural evolution and human activities, the relationship among the rivers and lakes has shown new characteristics, such as tremendous decline of sediment, decrease of diverted flow from Changjiang River, advancing of low water period, and continuous draw down of dry water level. Based on a systematic review on the evolution laws of the relationship between rivers and lakes and its impact on the water security of the two lakes, the key tasks for the governance and protection of the two lakes were discussed. Countermeasures were proposed, including orderly promoting comprehensive governance of the two lakes, improving the flood control, drainage, and disaster mitigation system, optimizing water resource allocation and water conservation measures, strengthening water environmental protection and governance, and enhancing water ecological protection and restoration. The research results can provide scientific basis and water security guarantee for the high-quality development of the Changjiang River Basin.