In this paper, the principle and steps for differentiating water masses by fuzzy cluster method are introduced, and a scalar formula based on Euclidean distance and a method for determining objectively the number of water masses by F-test are proposed.Consequently, a method and specific steps for differentiating modified water masses in shallow sea according to fuzzy elastic classification are given.Computation of the membership degree in which each sample belongs to every water mass determines conveniently and quantitatively the cores, boundaries of water masses and mixed zones.An example for the Huanghai Sea and East China Sea is shown and compared with previous results.