Ah, the ocean, a place full of symbolism.
In tales featuring pirates and swashbuckling duels, it represents freedom and a sense of adventure. Ghost stories show it as a place filled with dead and forgotten memories. And sometimes the ocean is a place of hardships and struggle. So, you know, life.
In Godzilla, the ocean's a place outside of the normal, separate from the domain of humanity. This is classic sea symbolism right here. The Odyssey showed Odysseus battle monsters and gods on his way home across the sea, H.P. Lovecraft's famous god-monster, Cthulhu, set up shop here, and many a mythological creature has made its domain in the unseen wet world beneath the surf.
Godzilla has a similar origin.
It started life as a prehistoric creature living undisturbed in the territorial waters off Odo Island, but its home was destroyed and it was injured after the U.S. tested an H-bomb in the Pacific. Enraged, this alien creature from another era transgressed "the boundary between that which is inside (land) and outside (the sea)" (Source).
As the movie progresses, Godzilla transgresses deeper into the inside and makes it inhabitable for humans. It moves from boats to island villages to the mainland to the heart of Japan itself, Tokyo. With each place it visits, the known and human is destroyed and the fearful unknown takes its place. Japan tries to keep the boundary between the inside and outside intact—at one point they literally build an electric fence to separate the two—but nothing works.
Later, Serizawa uses the Oxygen Destroyer to cast the unknown back into the mysterious sea. Although Godzilla tries to surface one more time, he's ultimately defeated by the device and sinks back to the mysterious depths.
The movie ends with two interesting shots regarding the symbolism of the ocean. The first is the shot of humans celebrating on a boat. They are on top of the water, having restored the boundary between the known and unknown. Humans are in control of their domain once again and safe.
But soon after, we see a shot of the ocean, serene but opaque. We can't see underneath it, and Yamane's warning that another Godzilla may rise again if we continue to test nuclear bombs hangs over the shot. Could another mystery lie beneath the ocean?
We shudder to think. What we already know is under there is horrifying enough.