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The optimal selection of schemes of water transportation projects is a process of choosing a relatively optimal scheme from a number of schemes of water transportation programming and management projects, which is of importance in both theory and practice in water resource systems engineering. In order to achieve consistency and eliminate the dimensions of fuzzy qualitative and fuzzy quantitative evaluation indexes, to determine the weights of the indexes objectively, and to increase the differences among the comprehensive evaluation index values of water transportation project schemes, a projection pursuit method, named FPRM-PP for short, was developed in this work for selecting the optimal water transportation project scheme based on the fuzzy preference relation matrix. The research results show that FPRM-PP is intuitive and practical, the correction range of the fuzzy preference relation matrix A it produces is relatively small, and the result obtained is both stable and accurate; therefore FPRM-PP can be widely used in the optimal selection of different multi-factor decision-making schemes.