The Feng‐Sang River is a metropolitan river in Kaohsiung City, Taiwan. In this study, Feng‐Sang River sediments were analyzed to investigate the distributions and sources of polycyclic aromatic hydrocarbons (PAHs). The Sediment Quality Guidelines (SQGs), potentially carcinogenic PAHs (TEQcarc), and toxic equivalence quotient (TEQ) were applied to evaluate influences of PAHs on ecosystems and microbial diversities. Results indicate that PAHs concentrations varied between seasons and locations. The concentrations of ∑16PAHs ranged from 73.6 to 603.8 ng/kg in dry seasons and from 2.3 to 199.3 ng/kg in wet seasons. This could be because of the flushing effect during wet seasons, which caused the movement and dilution of the PAH‐contaminated sediments. Diagnostic ratio analysis infers that high PAHs levels were generated by combustion processes and vehicle traffic, and results from multivariate descriptive statistical analysis also demonstrate that the vehicular traffic pollution could be the major emission source of PAHs contamination. Comparisons of PAHs with SQGs indicate that PAHs concentrations in sediment were below the effects range low (ERL) values, and thus, the immediate threat to organisms might not be significant. The diagnostic ratio analyses are effective methods for PAH source appointment. The metagenomic assay results imply that sediments contained essential microbial species with eminent diversity. The detected PAH‐degrading bacteria (Desulfatiglans, Dechloromonas, Sphingomonas, Methylobacterium, Rhodobacter, Clostridium, and Exiguobacterium) played a key role in PAHs biotransformation, and Dechloromonas and Rhodobacter had a higher relative abundance. Results of microbial diversity analyses indicate that the contaminated environment induced the changes of governing microbial groups in sediments. Practitioner Points Diagnostic ratio analyses are effective methods for PAHs source appointment. Microbial composition in sediments are highly affected by anthropogenic pollution. Combustion and vehicle traffic contribute to urban river sediments pollution by PAHs. Dechloromonas and Rhodobacter are dominant PAHs‐degrading bacteria in sediments.