Abstract In this work, the effect of phenanthrene and pyrene on biosynthesis and accumulation of bioactive ingredients of Sparganium stoloniferum Buch.-Ham. was evaluated. The analysis of phenanthrene and pyrene was performed using Gas Chromatography-Mass Spectrometry (GC–MS). The bioactive compounds were determined using different analysis technology. In the presence of pyrene and phenanthrene, this plant could grow well. The decreased or increased phenolics content could be observed in response to pyrene and phenanthrene. The low concentration phenanthrene and pyrene could enhance the accumulation of the mannitol and high concentration PAHs inhibit the accumulation. The accumulation of total saponins was not sensitive to pyrene and phenanthrene. To adapt the changes in environmental conditions the polysaccharides accumulation significantly increased. The findings obtained from this study will provide the science basis to investigate the accumulation of bioactive ingredients from plant in the presence of phenanthrene and pyrene.