Based on the limitations of the blue line planning of rivers and the actual demand of water protection in urban areas, the study constructs an evaluation system of the water protection works with the GIS spatial overlay analysis technology and the weight coefficients of five natural attributes and social attribute factors are determined by the AHP. The study gives an accurate and objective interpretation of the current situation of water area protection in Qinhuai District and delimitates more reasonable and practical water area protection boundaries based on blue line planning. The study overcomes the limitations of blue line planning, enhances regional pertinence and maneuverability and reduces the disturbance of various influencing factors in the urban areas to water quality and ecological stability, which has a great significance to enhance the protection and management of urban water areas.