Display omitted •185 out of 940 organic chemicals were found in river sediments in Vietnam.•Rivers were mainly polluted with chemicals originating from domestic sources.•Urban canals were heavily polluted with pyrethroid insecticides.•PAHs and OCPs compounds had concentrations exceed sediment quality guidelines.•This comprehensive analytical method is a useful tool for environmental surveys. In order to obtain a detailed picture of pollution by organic micro-pollutants in Vietnamese rivers, 940 semi-volatile organic compounds in river sediments collected from four major cities were examined by a comprehensive gas chromatography–mass spectrometry-database. The number of detected chemicals at each site ranged from 49 to 158 (median 96 out of 940) with 185 analytes detected at least once in the survey. The substances detected with high frequency (over 80%) and high concentrations were n-alkanes, phthalates, sterols and PAHs. For most substances, sediments from metropolitan areas (Hanoi and Ho Chi Minh City) were more heavily contaminated than those in rural and suburban areas. Sterols were observed in nearly 100% of sediments at extremely high concentrations, suggesting that the studied rivers were contaminated by sewage. Pyrethroids (permethrin-1 and -2) were the most dominant insecticides found in inner canals of Hanoi and Ho Chi Minh City. Deltamethrin was only detected at a site in Hanoi at an elevated concentration. This reflects that pyrethroids are used for the protection of private and public health rather than for agriculture. p,p′-DDE and p,p′-DDD were the dominant members of the DDT family of chemicals detected, indicating no recent inputs of DDTs in the study areas. PCBs residues were lower than those in other Asian countries, which suggest historically much lower use of PCBs in Vietnam. PAHs pollution in urban areas is caused by the runoff of petroleum products and vehicle exhaust gases, whereas in rural and suburban areas, the combustion of fossil fuels and biomass is major sources of PAHs. Overall, the study confirmed that rivers in Vietnam were heavily polluted mainly by domestic wastewater.