In all the books and games, I have never seen an aquatic vehicle used for military application. Given how efficient air vehicles seem to be in-game, it is probably because ships and boats are thus too limited in application.
One only has to look at the UNSC's Pelican and the Covenant's Phantom dropship to see the varied uses it has. Both appear to have significant range, high speed (hundreds of miles per hour), and are capable of suborbital space travel. Given that even a fast ship would be confined to a small body of water, not being able to travel more than a few hundred miles in a day, ships likely became obsolete years before the events of the human-covenant war.
I do remember vaguely a small skiff being used in one of the Kilo-Five books, but that was for a fishing trip I believe, not military applications. I don't remember anything about Forerunner watercraft larger than small skiffs, if any existed.
Edit: Thanks to PhilPursglove's answer, the small skiff is actually the Sanghelli Ocean Skimmer, which is not strictly a watercraft in that it actually hovers over the water. There are two human 'boats' listed that he found, and one is an actual boat, but the other is the Armed Assault Boat. The only mention of it comes from Halo: The Flood, and it does not appear to be much of a watercraft:
Most combat landings were made via armed assault boats, but the boats were slow, and subject to antiaircraft fire. That was why the UNSC had invested the time and money necessary to create a second way to deliver troops through an atmosphere: the HEV, or Human Entry Vehicle.
So there are some watercraft, they are just extremely rare.