“Fluorescence fingerprint” of water body based on fluorescence excitation-emission matrix has been a novel and valuable method to exhibit the organics details. In the present study, the fluorescence matrixes of urban water bodies of Beijing were investigated. The experimental results showed that these matrixes could be divided into 3 groups: Type I owned two fluorescence centers, locating at λex/λem=275～280/340 and 225～230/340 nm respectively, and was the predominant group; fluorescence centers of Type Ⅱ located at λex/λem=280/345～365 and 245/380 nm; Type Ⅲ had four fluorescence centers around 275/305, 275/340, 225/305 and 225/340 nm. The fingerprints indicated that these water bodies had been disturbed by human activities. Type I and Type Ⅲ were transitional fingerprints between undisturbed water body and sewage wastewater and Type Ⅲ was closer to sewage wastewater. Type Ⅱ closely originated from reclaimed water of municipal wastewater treatment plant. These three types were main types of urban water bodies where domestic pollution was dominating. The fluorescence fingerprints clearly displayed the ubiquitous impacts of human activities and the resulting potential risk. Fluorescence fingerprint could display pollution information and serve as a possible diagnosis tool of pollution source.