The availability of water resources is crucial to maintaining the sustainability of urbanization. Calculating the ecological footprint of water (EFW) is one of the ways to realize the protection of water resources in the process of urbanization. The minor settlements in border areas have been the focus of China’s urbanization development but have rarely received research attention. The objective of this study was to develop an improved model of the ecological footprint of water (EFW) to assess the water security status of urban areas in Yanbian Korean Autonomous Prefecture (YKAP), and to demonstrate its authenticity compared with the traditional ecological footprint of water (EFW). The results showed that water pollution is the main reason for the increase in the EFW in each city, and the ecological water carrying capacity (ECW) showed strong fluctuations with the interannual variation in precipitation. Although the overall availability and quality of water resources are within safe limits, there are significant differences among cities, and water pollution poses a direct threat to the health and well-being of urban dwellers in some cities. Therefore, it is recommended that water resource management agencies adjust their water supply strategies based on the data from the EFW model, control wastewater discharge, improve their management systems and take urban economic development into account. This will significantly improve the sustainable management of water resources and ensure the health and well-being of urban residents.