Bioavailability of benzo[a]pyrene (BaP) and 3,3′,4,4′-tetrachlorobiphenyl (TCB) was studied in natural lake water containing dissolved organic matter (DOM). Lake water was diluted to give a dissolved organic carbon (DOC) range of 1 to 20 mg/L. Partition coefficients for the model compounds were assessed at different DOM concentrations and over time with three different methods, namely equilibrium dialysis and reverse-phase and liquid-liquid extraction. In addition, biological partition coefficients were estimated from the difference in the bioconcentration of the model compounds in Daphnia magna in the presence and absence of DOM. Results showed that bioavailability of the model compounds was reduced by the presence of DOM. The equilibrium dialysis method gave the best estimates for bioavailability of the model compounds when compared with biologically determined values. Both the reverse-phase and the liquid-liquid extraction overestimated the bioavailable fraction. The more pronounced overestimation of bioavailable fraction of TCB suggested that the sorption of TCB was not only lower but the interaction was also weaker than that of BaP. Increasing DOM concentration produced lower partition coefficients and the effect seemed to be more pronounced when measured by the reverse-phase and the extraction methods.