Hexylene-bridged periodic mesoporous polysilsesquioxanes (HBPMS) are a promising new class of adsorbent for the removal of organic contaminants from aqueous solutions. These hybrid organic-inorganic materials have a larger BET surface area of 897 m2·g−1 accessible through a cubic, isotropic network of 3.82-nm diameter pores. The hexylene bridging group provides enhanced adsorption of organic molecules while the bridged polysilsesquioxane structure permits sufficient silanols that are hydrophilic to be retained. In this study, adsorption of phenanthrene (PHEN), 2,4-Dichlorophenol (DCP), and nitrobenzene (NBZ) with HBPMS materials was studied to ascertain the relative contributions to adsorption performance from (1) direct competition for sites and (2) pore blockage. A conceptual model was proposed to further explain the phenomena. This study suggests a promising application of cubic mesoporous BPS in wastewater treatment.