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Magnetic susceptibility and geochemical data have been widely used in environmental studies. In general, the data are analyzed only based on the correlation between variables. In this paper, the multivariate statistical analysis method is used intensively to identify environmental conditions based on magnetic susceptibility and geochemistry. The objects of this research are the two inlet rivers of Lake Sentani, namely the Hubay River and the Walker River. Using the method we found the characteristic of geochemical elements in the inlet rivers, which distinguishes the two rivers significantly.