With the aid of theory of landscape ecology, analysis of traj ectories and assessment of ecosystem service, this paper takes the water body in Shenzhen as the research object, analyzing the dynamic process of water body fragment and the corresponding changes of the ecosystem service. The results show that: 1) the process of water body fragment is so clear that the shrink of water body is the main characteristic. During 2000 and 2006, rivers became segment and channelization, pond and wetland were shrinking. In addition, the processes of fragment are different between each kind of water body. 2) The endpoint of the trajectories of change of water is developed land, and the changing process from water to developed land impose the trend of fragmentation and shrinking. 3) Water fragmentation restricts the ecological service. The direct service value increases continuously, while the indirect service value decreases, which leads to the increase of the proportion of the direct service value.