We demonstrate an ultra-sensitive waveguide-enhanced Raman sensor for low concentration organic compounds dissolved in water. The spectra are obtained using silicon nitride slot waveguides coated with a thin film of hexamethyldisilazane-modified mesoporous silica. Enriched locally by 600-fold within the coating, a micromolar level of cyclohexanone is probed. The sensor is also capable of simultaneous quantification of multiple analytes, and the adsorbed analytes can be completely released from the coating. These properties make this on-chip Raman sensor promising for diverse applications, especially for the monitoring of non-polar organics and biomolecules in aqueous environments.