Integrating surface enhanced Raman scattering (SERS) with microfluidics is the long-term goal for reduced volume, multiplex and automation fingerprint detection of biomolecules. High sensitivity, repeatability, stability, reusability and real-time detection are the performance goals of Raman detection in the aqueous solution environment. Here, we reported the study on cavity mode enhanced SERS detection of both surface-adsorbed molecules and non-surface-adsorbed molecules in the solution environment. The cavity modes had important influence on the SERS enhancement, especially for the non-surface adsorbed molecules. Uniform, repeatable, reusable and real-time Raman signal detection of the non-surface adsorbed Rhodamine 6G molecules was demonstrated. Our work is an important step for the practical on-chip microfluidic Raman detection applications.