The Atlas
I believe that the Atlas is quite accurate. Well it may not be exactly as
Tolkien envisioned it, but the gray areas have been filled in by the cartographers. Tolkien enjoyed a sense of secrecy concerning many of the ways of the world (he never describes
events in the far east, nor were his sketches of the area ever published - remember how two of the
Istari, the blue ones, went into
the east and no longer came into the
tales) The
maps are to scale and very detailed.
Middle Earth went through a number of geographical changes over the years. The world was very simple geographically when there were the two pillars which lighted the world. In the numerous
wars between
Melkor (aka
Morgoth) and the
Valar the land was torn apart. The last time this happened was at the end of the
second age when
Beleriand was flooded and
Numenor was lost under the sea. The lake that you speak of was part of the huge body of water by which the
Elves were born. I don't have my
books handy or I would give you their names.
Mordor was not always an
evil land (
Utumno and then
Angband were the
fortresses of Melkor), and
Sauron occupied it in
the third age because it was surrounded by
mountains. So the body of water was moved in the process of the changing landscape, probably by either Melkor or the Valar during the
First Age although I can't swear to that.