Effects of aggregation and surface chemistry of carbon nanotubes (CNTs) on the adsorption of three synthetic organic compounds (SOCs), phenanthrene (PNT), biphenyl (BP), and 2-phenylphenol (PP), were investigated using commercially available pristine and surface functionalized single-walled carbon nanotubes (SWNTs), and multiwalled carbon nanotubes (MWNTs). Theoretical calculations and nitrogen adsorption analysis results demonstrated that aggregation of CNTs led to a significant reduction in surface area (especially for the SWNTs), but a significant increase of pore volume (especially for the MWNTs) due to interstices trapped in the CNT aggregates. In contrast to the nitrogen gas adsorption, the liquid phase adsorption results indicated that the adsorption of SM by CNTs was controlled by available adsorption surface area rather than pore volume, and aggregation of CNTs was an unfavorable factor for the SOC adsorption. Surface functionalization of CNTs; improved their dispersion in aqueous solutions, but decreased their adsorption capacities for the hydrophobic SOCs, which was attributed to the formation of water clusters around the oxygen-containing functional groups. Molecular configurations of SOCs also played a role in their adsorption. For the planar PNT, the SWNTs showed significantly higher adsorption capacities and site energies than the MWNTs, whereas for the nonplanar SOCs the adsorption capacity and site energy differences between the SWNTs and the MWNTs became smaller with increasing concentration of SOCs.