Studies investigating the effect of carbon nanotubes (CNTs) on the bioavailability and toxicity of hydrophobic organic compounds in aquatic environments have generated contradictory results, and the influence of different CNT properties remains unknown. Here, the adsorption of the polycyclic aromatic hydrocarbon phenanthrene (70–735 μg/L) to five types of CNTs exhibiting different physical and chemical properties was studied. The CNTs were dispersed in the presence of natural organic matter (nominally 20 mg/L) in order to increase the environmental relevance of the study. Furthermore, the bioavailability and toxicity of phenanthrene to Daphnia magna in the absence and presence of dispersed CNTs was investigated. Both CNT dispersion and adsorption of phenanthrene appeared to be influenced by CNT physical properties (diameter and specific surface area). However, dispersion and phenanthrene adsorption was not influenced by CNT surface chemical properties (surface oxygen content), under the conditions tested. Based on nominal phenanthrene concentrations, a reduction in toxicity to D. magna was observed during coexposure to phenanthrene and two types of CNTs, while for the others, no influence on phenanthrene toxicity was observed. Based on freely dissolved concentrations, however, an increased toxicity was observed in the presence of all CNTs, indicating bioavailability of CNT-adsorbed phenanthrene to D. magna.