you can adjust the water height level for a cell in FNVedit.
http://i.imgur.com/csRiQ.png
In this picture, the water height is such a negative number because that cell doesn't have a body of water in it (it's effectively a Null entry. Setting the water height to 0 will actually cause problems though). To get an idea of a reasonable level for cells that do have water, you can browse the FalloutNV.esm in FNVedit and find a cell that you know has water (like the lake near Camp Gulf).
Yeah but you can also set the water height level for a cell in the geck itself. You just have right click on the cell in the cell view window and go to properties. But he would still have to adjust the land to be above the water again.
That said, unless anyone else show's up with another solution (which I have never heard of another in my almost 2 years experience here.
) you will have to restart with the appropriate default water height. Don't worry, this happened to me on my first exterior map, and I had to redo like 10-15 hours of work on the worldspace.