As the Brotherhood of Nod didn't have a Navy, the Global Defense Initiative possessed naval superiority. A Gunboat can fire one machine gun at enemy forces clearing for GDI's Navy to move on. Colonel J.C. Carter was presumed to be killed on a Gunboat at the Danube River in Hungary by some Obelisks of Light. Hovercrafts travel on water and land GDI reinforcements on beaches once all Nod presences have been cleared. The Hovercraft leaves the area after dropping off infantry or tanks. An Aircraft Carrier is the main hub for warplanes where they launch airstrikes against Nod forces in any area.
GDI still has naval supremacy with the return of both the Gunboat and Hovercraft. The newly introduced Helicopter carrier where Helicopters like the CH-46 Sea Knight land on the bow of the carrier and are the counterparts to the Aircraft Carriers. One of these was the headquarters for GDI's Command Center led by Adam Locke to end control from the Brotherhood on Earth.
Nod finally got their own Navy. A Nod submarine fires torpedoes at GDI shipping whenever they are sighted, while a Nod freighter is the main pride for the Brotherhood and Nod submarines once escorted the freighter to its location. It held three GDI prisoners and the freighter was led by Stuving and his first mate Gilligan.
The GDI Navy consists the Battleship for artillery barrages from Sniper teams as artillery spotters, Aircraft Carriers like GDS Pathe at Hampton Roads Naval Base and the unknown one at the Atlantic Coast of Brazil and Hovercrafts to land GDI or Nod forces at their destinations like GDI's one in Alexandria to land two Mammoth 27s after destroying Nod's Battleships.
The Brotherhood had three Battleships in different locations: one in Chile to kidnap Alphonse Giraud and destroying GDI's base there, while two Battleships were in Alexandria and were destroyed. A Hovercraft was used in Australia by Nod to land their forces on the beach as GDI prepares to get rid of the Nod presence.