Is there a Minecraft Command with which you can only replace water with air in one area, without having to delete other buildings?
It's called world edit
Is a plugin / mod and is called World Edit.
Then select the area with the wooden ax and use this command:
// replace water air
Yes there's:
/ fill x1 y1 z1 x2 y2 z3 minecraft: air replace # minecraft: water
to Info: This command works wonderfully in 1.13 and 1.14. I do not know if this command goes so well in older ones. Maybe you have to omit the #