Zhangjiakou region is situated in an agro-pastoral ecotone with a fragile ecosystem. While it has limited surface water resources available and serious groundwater over-exploitation, the city is located in the water conservation zone for the Beijing-Tianjin-Hebei coordinated development area, so its water security is crucial for the entire Beijing-Tianjin-Hebei region. Therefore, it is of vital significance to determine the zoning management of water resources and decision-making according to the magnitude of water resource security risks. This study built an indicator system for water security risk assessment in line with the principles of scientific validity, comparability, operability, and data availability, and this system gives weights to these indicators using the AHP approach. County-level multi-source data for the study area, based on water resource zones, were collected by using mathematical statistics and 3S technology. With normalized data and a weighting method the water security risks were calculated. The results showed large spatial variations of water security risks in Zhangjiakou on the scales of geomorphic and administrative units as well as river basins. High-risk areas are extensive in the Bashang Plateau, and extremely high risk values are found in the Baxia areas. On the watershed scale, high-risk areas are mainly distributed in the inland river basins and the Yongding River basin. The risk values of the Luanhe River, Chaobai River and Daqing River basins in the Zhangjiakou region tend to decrease from north to south. For the northern and western areas of the Bashang Plateau, the factor of “vulnerability of the disaster-prone environment” contributes the most to the water security risk level. Agricultural water use constrains industrial and ecological water use, but in the context of inadequate water resource endowments, the urban population concentration and industrial development are the main causes of water shortages and water pollution so they contribute more to water security risks. This study of the spatial variation of water security risks in Zhangjiakou can provide an important scientific reference for zone-based management and decision-making for reducing the water security risks in the farming-pastoral ecotone.