Biological aerated filter was used to treat eutrophic river water at different filler mass ratio and temperature on the removal of contaminants. The filter contained a functional composite filler which was made of activated iron and ceramsite. The results showed that the reactor was stable after 30 days of start-up at room temperature and that the proportion of filler mass exerted little effect on COD removal. At different temperatures, the denitrification and phosphorus removal capacity of reactor #1 was better than that of reactor #2, in which the composite filler with an activated iron and ceramsite mass ratio was 1:1(reactor #1) and 1:3 (reactor #2). At 10ºC, both reactor #1 and #2 had removed COD, TN and TP effectively. The relative abundance of species and the diversity of microorganisms in reactor #1 were higher than those in reactor #2. According to the analysis at the phylum and the genus level, bacteria with nitrification and denitrification functions in #1 and #2 were dominant and the proportion of activated iron affected the distribution of microbial population.