This study aimed to investigate the removal of 24 semivolatile organic compounds in Yangtze River (China) source water treated by six biofilters using different backwashing methods. Health risks induced by the pollutants in the influent and effluent water were also assessed based on the chemical detections. Comparatively, the biofilter backwashed with both air (15 m/h, 3 min) and water (8 m/h, 5 min) was most efficient in removing semivolatile organic compounds and reducing health risk. PCR-denatured gradient gel electrophoresis showed that backwashing alterations posed considerable influences on microbial community structure in the six biofilters. About 72.4 % of di-n-butyl phthalate and 81.8 % of bis(2-ethylhexyl)phthalate (two main semivolatile organic compounds in the river water) were removed under the optimal backwashing conditions. However, in the effluent of each biofilter, non-carcinogenetic risks of 2,6-dinitrotoluene and bis[2-ethylhexyl]phthalate and carcinogenetic risks of dibenz[a,h]anthracene and benzo[a]pyrene did not reach safety levels, revealing that these pollutants in the source water deserve more public health concerns. This study might serve as a basis for biofiltration process optimization and also as a benchmark for the authorities to reduce the health risk induced by exposure to the hazardous pollutants.