While water vapor transmission rate (WVTR) measurement is standardly used to assess material permeability, a system able to quantify liquid water transmission rate (WTR) measurement is highly desirable for implantable thin film barrier coatings. Indeed, since implantable devices are in contact or immersed in body fluids, liquid WTR was carried out to obtain a more realistic measurement of the barrier performance. Parylene is a well-established polymer which is often the material of choice for biomedical encapsulation applications due to its flexibility, biocompatibility, and attractive barrier properties. Four grades of parylene coatings were tested with a newly developed permeation measurement system based on a quadrupole mass spectrometer (QMS) detection method. Successful measurements of gas and water vapor and the water transmission rates of thin parylene films were performed and validated, comparing the results with a standardized method. In addition, the WTR results allowed for the extraction of an acceleration transmission rate factor from the vapor-to-liquid water measurement mode, which varies from 4 to 4.8 between WVTR and WTR. With a WTR of 72.5 µm g m−2day−1, parylene C displayed the most effective barrier performance.