A roof mounting system for installing a plurality of PV modules on a roof surface includes a waterproof base mount assembly for attaching to a roof surface. The waterproof base mount assembly includes: a base member having a top surface comprising a waterproofing means consisting of an upstanding portion that extends away from the roof surface, the upstanding portion defining a distal end aperture; a block member having an elevated seal portion configured to fit over the base member, a through hole configured to fit over the upstanding portion of the base member and a vertically extending engaging portion; a tightening means for attaching the base mount assembly to the roof surface by insertion through said through hole and said distal end aperture; and, a sealing washer for fitting on the tightening means and adapted to seal the through hole in the elevated seal portion to prevent seepage of water. The system further includes a clamp assembly for connecting a frame member of at least one PV module to the base mount assembly, and a structural member having a top portion for connecting to the clamp assembly and a bottom portion for connecting to the vertically extending engaging portion of the waterproof base mount assembly.