The research on water masses is always one important facet of Oceanography. I adopt the method of Fuzzy Density Clustering to analyse water masses. Meanwhile, I use Visual Basic 6.0 as developing platform and utilize the MapX components to develop the platform of GIS. By integrating the Water Masses Model compiled by FORTRAN language, and GIS using Tight Coupling, I develop an Integrated System. That makes all phases are finished in one condition, including the gain of computing grid, the pick-up and analysis of data, the choice of parameters and resetting, the computing of model, and the result's visualization. It improves the efficiency of the data analysis and decision-making Finally, this system is applied in the Zhoushan fishing ground and adjacent region. The results are satisfying.