Polybrominated diphenyl ethers (PBDEs) are a class of widely used brominated flame retardants with strong hydrophobicity. Due to their strong affinity for organic matter, accurate measurement of adsorption coefficients for PBDEs using conventional batch methods can be confounded by biases caused by their sorption to dissolved organic carbon (DOC). In this study, sorption isotherms were constructed for BDE-47 and BDE-99 in sediments by using different methods to measure the aqueous phase concentration Cw. Upon centrifugation, Cw measured by automated solid-phase microextraction (Cw-SPME) was consistently smaller than by liquid-liquid extraction (Cw-LLE), suggesting substantial association of PBDEs with DOC. Significant underestimations (1.2-106-fold) of sediment-water partition coefficient Kd occurred when Cw was measured by LLE. The log KDOC values derived from the SPME measurements ranged from 5.10 to 8.02 for eight congeners from BDE-28 to BDE-183, suggesting a strong tendency for PBDEs to complex with DOC. This study showed that PBDE congeners have larger sorption coefficients than would be measured by the conventional method. The high affinity to DOC also means a potential for DOC-facilitated transport, thus enhancing the environmental mobility of PBDEs.