Can I bypass one Bolt on my water pump

Depends on the bolt, which engine you have, etc. Is there enough that you can weld a nut to the remaining bolt? All you need is if it's broken off flush, I can describe how to weld a nut to it.

Drilling it out is another possibility but that almost always ends in a disaster. Some bolts go into the cooling system and had sealer on the threads. If you drill those there's a good chance they will leak later. Have you ever used "Easy Outs" or Heli-Coils?

In some applications you can even drill and tap a new hole next to the old one.