a b s t r a c tPolycyclic aromatic hydrocarbons (PAHs) are likely to transform to more mutagenic and carcinogenic substituted polycyclic aromatic hydrocarbons (SPAHs) in the environment. To date, no literature has reported on an analytical method for SPAHs in the natural water environment (encompassing water, suspended particulate and sediment matrix). A robust and routine analytical method was developed for simultaneous detection of 13 typical SPAHs and 16 PAHs in the water environment in this work. The pretreatment and instrument analysis procedure were optimized for effective detection of the 29 targets species. Recovery of each target ranged from 60% to 120%, except for benz [a]anthracene-7,12-dione (BA-7,12-D), which resulted from the transformation of 7-nitrobenz[a]anthracene (7-NBA). The high recovery of BA-7,12-D was relatively stable, so the detection results could be corrected. The method quantification limits ranged from 0.04 ng/L to 20.25 ng/L for 4 L water samples, from 4.12 ng/g to 131.66 ng/g for 0.1 g particulate samples, and from 1.75 ng/g to 28.04 ng/g for 20 g sediment samples. The method was applied to detect the 29 targets pollutants in polluted rivers, receiving wastewater from Beijing and Tianjin in China. Certain SPAH targets including 2-methylnaphthalene, 2,6-dimethylnaphthalene, 1-methylfluoranthene, 3,6-dimethylphenanthrene, 9-fluorenone, anthraquinone, 2-methylanthranquinone and BA-7,12-D were detected in the natural river environment, and all PAH targets were found in rivers.