This work investigated soil samples collected from Kuan-Tu wetlands, Taiwan. Factor analysis was performed to explain the impact of various soil factors on this marshy wetlands located in suburban Taipei. The results indicated that the latent factors were heavy metals, salinity, and soil organic matter. Canonical discriminant analysis was used to improve an existing vegetation classification scheme by identifying the physical-chemical properties of sediment in Kaun-Tu wetlands, Taiwan. Predictive discriminant analysis was used to examine the ability of the models to predict class membership for unknown soil sample. Multivariate analysis of the spatial patterns of soil quality and vegetation types showed that different properties of soil grew different types of vegetation and absorbed contaminants differently. We can feasibly conserve a suitable habitat for wetland biology by processing these unstable predictor variables. The methodology and results provide useful information concerning the Kuan-Tu wetlands and may be applicable to other wetlands with similar properties that are experiencing similar environmental issues.