In this paper, we present a new chromatographic method termed surface-bubble-modulated liquid chromatography (SBMLC), that has a hybrid separation medium incorporated with surface nanobubbles. Nanobubbles or nanoscale gas phases can be fixed at the interface between water and a hydrophobic material by delivering water into a dry column packed with a nanoporous material. The incorporation of a gas phase at the hydrophobic surface leads to the formation of the hybrid separation system consisting of the gas phase, hydrophobic moieties, and the water/hydrophobic interface or the interfacial water. One can change the volume of the gas phase by pressure applied to the column, which in turn alters the area of water/hydrophobic interface or the volume of the interfacial water, while the amount of the hydrophobic moiety remains constant. Therefore, this strategy provides a novel technique not only for manipulating the separation selectivity by pressure but also for elucidating the mechanism of accumulation or retention of solute compounds in aqueous solutions by a hydrophobic material. We evaluate the contributions of the interfacial water at the surface of an octadecyl bonded silica and the bonded layer itself to the retention of various solute compounds in aqueous solutions on the column packed with the material by SBMLC. The results show that the interfacial water formed at the hydrophobic surface has a key role in retention even though its volume is rather small. The manipulation of the separation selectivity of SBMLC for some organic compounds by pressure is demonstrated.