This study aimed at the pollution problems of organic matter, algal and nitrogen pollution in drinking water sources, the biological aerated filter (BAF) was used to treat micro polluted source water. The removal effects of NH₃-N, TN(total nitrogen), TP(total phosphorus), CODMn, Chl-a, UV₂₅₄ under the different hydraulic load were examined. The results showed that the average removal rates of NH₃-N, TN, TP, COD_Mn, Chl-a, MC-LRand UV254 were 74.71%, 46.55%, 81.8%, 52.16%, 67.99%, 79.2% and 34.8% respectively at the hydraulic loading of 0.07m³/(m²·h). The minimum effluent concentration of NH₃-N, TP, CODMn met Ⅱ class national standard of Surface Water Environmental Quality Standards(GB 3838-2002). The analysis of biological microscopy and high-throughput sequencing (454) showed that the microbial community on the biofilm of BAF was extremely rich in the micro-polluted source water of low carbon source. At the early stage (the first 2 weeks), the microflora on the biofilm had 17 major genera and 6 species. At the later stage (3 to 4 weeks later) the microflora increased to 43 major genera and 14 species. Protists such as nematodes, paramecium and daphnia, were also observed. The dominant species were Sphaerotilus (2.41%~24.58%), Aeromonas (4.16%~12.59%), Cloacibacterium(1.85%~12.39%), Aquabacterium (1.53%~6.76%), Hydrogenophaga (1.12%~5.9%), Methyloversatilis (0.53%~1.52%), Rhodobacter (0.09%~1.39%). Microbial degradation is mainly responsible for the treatment of organic matter and nitrogen pollution in drinking water sources by BAF. The physical filtration, adsorption and ion exchange of zeolite also play an important role in the treatment of organic matter and nitrogen pollution in drinking water sources. A high removal ratios for nitrogen, phosphorus and algae pollutants can be achieved in BAF. This study has certain theoretical significance and engineering application value for biological pretreatment of micro polluted source water.