We present a design for integrated lab-on-chip microsystems dedicated to mass spectrometry analysis based on the fabrication of watertight microchannels for the circulation of liquids. In this paper, we demonstrate how to fabricate complete polymer microchannels using the negative photoresist SU-8 which has the advantage of being compatible with protein analysis by mass spectrometry. Our method of fabrication requires novel technological steps involving SU-8 multi-layer processing, improved SU-8 adhesion and the use of SU-8 wafer bonding for the watertight closing of the microchannels with a Pyrex wafer. This technique also encompasses the design of various microfluidic elements such as tapered recesses for the housing of capillary tubes allowing the connection of the channels to external systems. Following this, the capillary tubes were used to test the hydrodynamic behaviour of the channels and consequently the efficiency of our technological process in achieving fully watertight structures within our flow rate and pressure specifications.