Partition coefficients of polynuclear aromatic hydrocarbons (PAHs) between biodiesel fuel mixtures (i.e. B1, B5, and B20) and water were determined by the frequently applied estimation method of Raoult’s law. The experimental partition coefficients were compared with calculation by polyparameter linear free energy relationship (PP-LFER) approaches. Deviations from poor recovery of PAHs from the aqueous phase in partition experiments and parameters in the PP-LFER equation are discussed. The results suggest that the extent of deviation from ideal behaviour for biodiesel–water partitioning is relatively small (i.e. errors remain within a factor of two). The concentrations of PAHs in water in equilibrium with these biodiesel fuel mixtures, estimated from the model presented, may be considered as a reasonable approximation for most field-scale applications.