The sensitivity of a waveguide-mode sensor, which has a sensing plate incorporating a thin single-crystalline Si layer and a thin SiO2 glass layer on a silica glass substrate, can be improved by increasing the surface area of the thin SiO2 glass layer by forming nanopores. In this study, we achieved the highly sensitive detection of surfactants in water by hydrophobic treatment of the surface of the sensing plate on which nanopores were formed. The hydrophobic treatment ensures that no water enters the nanopores, even when the sensing plate surface is immersed. When a surfactant is present in the water, the surfactant is gradually adsorbed on the sensing plate surface, which leads to hydrophilization; the water can then enter the nanopores. This results in a large refractive index variation on the chip surface, which makes it possible to detect the surfactant with high sensitivity. 0.02 mg/l Tween 20, which is a nonionic surfactant, and 0.02 mg/l sodium dodecyl sulfate, which is an anionic surfactant, were successfully detected using this sensor.