[Objective] The plankton and macrobenthos samples in municipal polluted river were analyzed by different methods, so as to explore the method suitable for biological data analysis in heavy polluted area. [Method] Shannon-Wiener diversity index, cluster analysis of multivariate statistical analysis and MDS （Non-matric Multi- dimentional Scaling）analysis were used to analyze biological data of phytoplankton, zooplankton and Zoobenthos collected from the representative municipal polluted river in Pearl River Delta. The sediment samples were also collected to determine. Pb, Cd, Hg, Cr, As, Cu, Ni, Zn, as well as CODe, and NH3-N of porewater. Hakanson potential ecological risk index method was used to evaluate the ecological risk. [Re- suit] Shannon-Wiener diversity index analysis results can not effectively reflect the difference of pollution status of various stations in heavy polluted area; despite the presence of some problems, multivariate analysis method is superior to the Shannon-Wiener diversity index method in biological monitoring of heavy polluted river in the city. [Conclusion] The paper provided theoretical basis for biological data analysis in heavy polluted area.
