well, it's a hard thing to do. You could fill in the area of the tunnel with sand to the surface, getting rid of the water above it. then you can remove all the sand up to edges and build on dry land. Only problem is that it's gonna be hard to fill the water back in above it. For my glass tunnel, I swum down, dug a couple blocks, got more air, and repeated lots and LOTS of times, and then I constructed the tunnel under the water. Don't worry about removing the water until you are finished, the water sources are only on the surface of lakes and oceans. When you have finished the tunnel, find a way to block water from flowing in and PRESTO! you have an underwater glass tunnel.