Water is restrictive resource in the Yellow River Basin, North China Plain and the estuary delta. As a key part affecting the long-term safety of the lower Yellow River, the estuary needs to be comprehensively controlled coordinating with water and sediment. On the basis of estuary outlet optimization, engineering measures and possible impacts for the storage, protection, allocation, and utilization of freshwater are proposed. An estuary comprehensive management plan is proposed, which includes building a gate control and regulation hub on the mainstream at Xihekou, constructing large-scale reservoirs in Laizhou Bay and along the west Bohai Gulf, and laying out protection systems and related service systems along the delta and gulf reservoirs. The research results show that the plan can stably recover 10 billion m³ of high-quality fresh water, provide sufficient regulating storage capacity and convenient water distribution system, while ensuring flood control, sediment reduction, and the delta stability. It helps to improve the water and sediment regulation mechanism of the Yellow River, maintain the downstream sediment transport water, ensure long-term siltation reduction in the river channel, promote prosperity of the estuarine wetlands, and alleviate water shortage in the pan delta area, creating basic conditions for high-quality development in the pan delta area for the future.