In order to solve the prominent problem of water ecological security in Changsha-Zhuzhou-Xiangtan urban agglomeration, a comprehensive water security pattern was constructed and the location and type of GAP were analyzed based on ArcGIS and GAP analysis. The results show that the water security pattern in the core area of Changsha-Zhuzhou-Xiangtan urban agglomeration consists of three patches of water ecological protection zones with the total area of 256km², water ecology blue line corridor with the total length of 654 km and water ecology green line corridor with the total length of 516km. Flood risk and groundwater resources destruction risk are the most prominent water security issues in the study area, followed by the problem of wetland biodiversity conservation. There are three protection GAPs and two repair GAPs in the water ecology reserve, seven repair GAPs in the water ecology blue line corridor, two protection GAPs and ten repair GAPs in the water ecology green line corridor. These GAPs are short boards that determine overall safety in the water security pattern, and need to be prioritized in the next step of ecological construction.