The effects of the surfactants, Tween 80 and sodium dodecyl benzene sulfonate (SDBS) on a membrane’s fatty acid composition and the transmembrane transport of phenanthrene were investigated. The results indicated that both surfactants could modify the composition of fatty acids of Citrobacter sp. Strain SA01 cells, 50 mg L−1 of both surfactants changed the composition of the fatty acids the most, increasing the amount of unsaturated fatty acids. The comparison of fatty acid profiles with diphenylhexatriene fluorescence anisotropy, a probe for plasma membrane fluidity, suggested that an increased amount of unsaturated fatty acids corresponded to greater membrane fluidity. In addition, increased unsaturated fatty acids promoted phenanthrene to partition from the extracellular matrix to cell debris, which increased reverse partitioning from the cell debris to the cytochylema. The results of this study were expected in that the addition of a surfactant is a simple and effective method for accelerating the rate-limiting step of transmembrane transport of hydrophobic organic compounds (HOCs) in bioremediation.