River waters and wastewater treatment plant effluents contain hydrophobic organic compounds (HOCs) such as polycyclic aromatic hydrocarbons (PAHs) which are persistent, bioaccumulative, and dangerous for the environment. The biological risk assessment of HOCs requires the estimation of their bioavailable fraction in addition to the total contamination of the media. The bioavailability of HOCs depends on the characteristics of the aquatic environments. In particular, the presence of organic matter (OM) usually reduces the bioavailability of HOCs by trapping them and preventing them from crossing biological membranes. The semipermeable membrane device (SPMD) technique is used to evaluate bioavailable fractions of HOCs. We tested the influence of aquatic and more particularly OM characteristics on the SPMD-availability of PAHs, in several river waters (up and downstream a large town) and in wastewater treatment plant effluents. Thirteen priority PAHs were analyzed in total water and in SPMDs. Aquatic environments were characterized for their pH, ionic strength, temperature, chlorophyll A, and suspended solids contents. Total and dissolved OMs were characterized for aromaticity, biodegradability, molecular weight, and hydrophobicity. The total PAH contamination increased downstream the river; wastewater effluents were proven to be a source of SPMD-available PAHs. We attempted to establish relationships between the characteristics of organic matter and the SPMD-availability in order to initiate an aquatic environment typology: The SPMD-availability was negatively related to dissolved OM molecular weight and aromaticity, and positively related to biodegradability.