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I've played most of the games in the Halo series but not read the books or anything so I can't speak for those.
I've noticed that the vehicle sets in the games seem to only include land and air. However, there are still large water bodies in the games. Also, given that Earth is mostly water, it would seem like a logical option for an alien race attempting a take-over to have a way to get around on it.
Are there any aquatic vehicles in the Halo universe?
From the Halo wikia section on watercraft:
Few watercraft exist in the Halo story-line, however, those which are mentioned have helped to play a vital role within the installments.
Three boats are listed in its Watercraft section; two appeared in books and the third was deleted from Halo: Combat Evolved.
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.
Halo concept art books and the games depict watercraft. However their overall relevance to combat play except in littoral warfare or where the Spartans or ODST's must cross water. With the UNSC possessing spacecraft capable of planetary and atmospheric travel questions the validity of an ocean going naval force when the space capable ships are presumably faster. Ocean going ships are limited to speeds no more than 30-40 knots, faster with various exotic propulsion methods or hull configurations. Concept art and graphics do detail the UNSC as possessing ocean going warships in a so called "Wet Navy". ON the other hand there might be some benefit of ocean going ships. Said ships if were presumably powered by the same energy source as their spaceborne cousins (deuterium fusion) they'd probably mount the same weapons, namely MAC guns and missile pods would serve as mobile line of defense against invasion craft or ships trying to come in atmosphere. The ships can also be augmented with UNSC directed energy weapons (lasers) far larger than the M6 Spartan Laser. An ocean going vessel doesn't require a huge amount of power either just to stay airborne, it merely floats.
