Ordinary biomatter is very close to the density of water to begin with. That’s why having a little air in your lungs is enough to be the difference between sinking and floating.
If Godzilla’s biomatter under 1atm of pressure has a density close to water then being able to compress or expand an empty chamber inside his body by even just a tiny percentage of his ordinary overall volume could be the difference between floating at sea level or sinking to extreme depths.
Or if you prefer we can imagine that Godzilla gives himself a big ole booty when he needs to come up to the surface and make a mess of things.