In the first Matrix film, we see how Morpheus shows Anderson the devastated Earth, first from a TV screen, then like being actually there, looking on a city that looks like New York (the destroyed buildings look like the former WTCs). If it's indeed New York, it looks like they're watching it from a dried out Atlantic Ocean. Throughout the 2nd and 3rd film, the Logos goes from Zion to the Machine City eventually, leaving the underground tunnels close to the machine city and the fields and towers of the bluepills. Since I suspect Zion somewhere beneath North America and the Machine City is in Mesopotamia, either the tunnels are so deep they go beneath the Atlantic Ocean or there are no more oceans on the Matrix Earth.
It is assumed that Zion isn't "close to the Earth's core" as Tank put it, but much closer to the surface. Throughout the trilogy no surface water is seen (outside the Matrix), so are there no more oceans on the Matrix Earth and if so, how did that happen?