The designed device mainly consisted of combined packing, Cannas, and aquatic animals. Water from Suining Creek, a tributary of the Suzhou Creek in Shanghai, was used as experimental water. Differences of microbial amounts on plant roots and packing biofilms in the device was analyzed to find the mechanisms of microorganisms in the system. The resluts show that the mineralization, amination, nitrification and denitrification may complete at the same time, with the mineralization, amination, nitrification mainly on the surface of plant roots, and the denitrification mainly on the filling material. The plant roots and the filling material provide appropriate natural environment for heterotrophic bacteria, nitrifying bacteria and denitrifying bacteria. The total amounts of heterotrophic bacteria on the surface of per unit mass plant roots are about ten times more than those on the surface of the filling material. Plant could provide root with oxygen, hence, nitrifying bacteria amounts on the surface of per unit mass roots and of the filling material are: roots＞filling material of experimental group＞filling material of control group. But for the denitrifying bacteria, it behaves: filling material of control group＞filling material of experimental group＞roots. The amounts and types of microfauna on roots are more than those on the packing films, whose diversity index were 2.16 and 2.08 respectively.