In this study, time series analysis and factor analysis of multivariate analysis were applied to surface water quality monitoring data sets. In order to gain a better understanding on water pollution situations and sources of different river basin, we have done some statistical analysis according to the water quality monitoring data from the database of Environmental Protection Administration Executive Yuan in the years from 2004 to 2008. The statistical analysis is based on the aforementioned contents to find the common latent factors of the water pollution and try to explain the main sources of water pollution of river basins. Specifically the water quality monitoring data of the Tamsui River and the Kao-Ping River basin are analyzed. In seriously polluted areas, from the time series results they reveal that the water quality monitoring data has significant serial correlations. Therefore we firstly use vector autoregression (VAR) model to eliminate the dynamic dependencies of data, and later perform the factor analysis for the residuals. With this analysis procedure, the resulting models and factor variables from the factor analysis, sufficiently explained water quality variables with the potential relationship between environmental pollution in the region.