In the current study, the removal of slowly degradable hydrophobic chemicals in sewage treatment plants (STPs) has been evaluated with emphasis on the combination of free and total concentration data. Free and total concentrations of two polycyclic musks were determined in each compartment of four STPs. The free concentration of the polycyclic musks remains virtually constant throughout all the compartments of the STPs with values between 0.21 and 0.57 μg/L for AHTN and between 0.79 and 2.0 μg/L for HHCB. Total concentrations of these fragrances are highly dependent on the volatile solids in a given compartment resulting in much more variation with values between 0.42 and 92 μg/L for AHTN and between 1.25 and 258 μg/L for HHCB. It is concluded that free concentrations of these hydrophobic chemicals in the compartments of STPs are mostly biodegradation mediated, while total concentrations are mediated by the concentration of solids. The combination of measurements of free and total concentrations can improve estimations regarding removal efficiency and removal pathways.