A unified co-evolutionary model was developed to study the adaptability conditions of regional water security systems, which is important for the coordinated development of these systems. In this work, the main factors that affect the adaptability of regional water security systems, the contribution of each sub-problem domain to the development of the problem domain, and the fitness values of regional water security systems were analyzed based on the model. Taking Jiansanjiang as an example, the results showed that in 2002–2011, the water resources system had strong adaptability and contributed greatly to improve the adaptability of the water security system; the socioeconomic system had poor adaptability to environmental changes and contributed little to the adaptability of the water security system; and the eco-environmental system was barely able to adapt to the changing environment and contributed less to the adaptability of the water security system. Due to the influence of the socioeconomic and eco-environmental systems, the adaptability of the water security system was relatively weak. Therefore, strengthening the sustainable utilization of water resources, promoting the coordinated development of the social economy, and improving the quality of the ecological environment are effective strategies to improve the adaptability of water security systems.