A biofilm reactor was developed to investigate the sorption of polycyclic aromatic hydrocarbons (PAH) as model compounds for hydrophobic organic contaminants (HOC) to intact microbial biofilms at environmentally realistic concentrations. When operated as a differential column batch reactor, the system can be used to study the thermodynamics as well as the kinetics of the exchange of HOC between an aqueous phase and microbial biofilms. Organic carbon normalized partition coefficients (Koc) for phenanthrene, fluoranthene and pyrene were at the lower end of those known for other organic sorbents. Intra-biofilm diffusion coefficients (D) were calculated from decrease in solute concentration over time using a model for diffusion through a plane sheet and ranged from 0.23 to 0.45×10−9 cm2 s−1 for the three PAH. These diffusion coefficients are about four orders of magnitude lower than those reported in literature for free aqueous solution. These data and the experimental approach presented here are useful to assess the importance of microbial biofilms for exchange processes of HOC in heterogeneous systems such as water distribution systems, membranes and aquifers, sewer systems or surface soils.