Actually, what it looks like is some sort of cell error, possibly related to having too much of a height difference between the landscape points in that cell. Unfortunately I'm quite sure what I'm looking at as to what those square blocks are. If they're water, it could simply mean that you tried taking a shortcut to landscaping by moving all the water below 0 height, which would certainly cause this sort of thing in any cell where the water level was not changed or defined.
Having the http://i279.photobucket.com/albums/kk146/TheMagicianFromOblivion/missingwater.jpg is a very common bug. It occurs in cells adjacent to the last altered cell in a worldspace. You can fix these errors by making a change to the cell, but be aware that this will simply push the error back to the next cell and every cell you add to your worldspace increases the size of your mod. If you don't want a player to see this at the edge of your worldspace, use a border to prevent them from getting close to it.
Tears in the landscape, like those referred to by Vagrant0, are caused by having too sharp a change in elevation between cells in your heightmap. It's hard to tell what exactly is happening from the pictures, but I don't think this is the problem here. If making an alteration to the cell doesn't fix your problem, smooth the elevation in your heightmap.
You can fix that in landscape editing (Hkey). Just manually raise the land (flaten vertices) and the hole is gone, Save after . If you get the error, try again. This always work for me.