Effect of content of sediment organic matter (SOM), the main carrier of organic contaminants, on dissipation of phenanthrene and pyrene in sediments by Potamogeton crispus L. (P. crispus) was investigated. After a 36-day experiment, the dissipation ratios of phenanthrene and pyrene were improved by P. crispus but decreased with increasing SOM content no matter with or without P. crispus. The total dissipation enhancements of phenanthrene and pyrene by P. crispus were 9.35% and 9.02%, 12.47% and 10.34%, 13.60% and 10.95%, respectively, when their respective SOM contents were 1.20%, 3.14% and 5.08%. Furthermore, polyphenol oxidase activity was measured and bioavailability of the contaminants in sediments was calculated by a two-compartment desorption model. The results showed that they were both higher in planted treatment than in unplanted treatment. At the end, the enhancements of rapidly desorbing fraction (i.e. the main portion to be readily biodegradable) in sediments with SOM contents of 1.20%, 3.14% and 5.08% by plants were 20.0%, 40.7% and 66.7% for phenanthrene, 22.2%, 36.8% and 58.8% for pyrene, respectively. This is consistent with the change trends of dissipation enhancements of the two PAHs in sediments. However, there was no significant correlation between the enhancement of polyphenol oxidase activity and the enhancement of PAH dissipation ratio. These suggested that bioavailability enhancements by P. crispus should be the key factor leading to the dissipation enhancements of the two PAHs in sediments with different SOM contents.