Pyrethroid insecticides are widely used in both agricultural and urban environments. Pyrethroids have been frequently detected in California, USA, stream bed sediments. Pyrethroids are strongly hydrophobic so their bioavailability is determined by their sorption to sediment. In the present study, we used disposable polydimethylsiloxane (PDMS) fibers to sample from the freely dissolved (effective) permethrin concentration that governs bioaccumulation and toxicity, and tested the correlation of those measurements with uptake by Chironomus tentans. In sediments that were incrementally diluted with silica sand, both PDMS fiber and organic carbon (OC) normalized sediment concentrations were highly correlated with C. tentans permethrin uptake. However, for multiple sediments with OC ranging from 1.4 to 27%, C. tentans permethrin uptake showed a better correlation with PDMS fiber concentrations than sediment OC-normalized concentrations. We conclude that the qualitative properties of sediment OC influence permethrin phase distribution and therefore the bioavailability of permethrin in sediment–water systems. Consequently selective methods such as PDMS fibers yield improved estimates of bioaccumulation and toxicity as such methods detect freely dissolved permethrin concentrations in the sediment.