You just need to place a polygon including at least parts of the disturbing lakes. ADE will ask for the properties and you need to select "Exclude general" and then "Water Polys". The lakes should disappear. For getting rid of the shorelines you may want repeating this procedure, except you want to select "Shorelines" for this one. That's it.
As just removing would destroy the landscape in this case, I propose to catch a background picture for ADE and to redraw lakes and shorelines at their correct position. The proper tool for taking the picture is
here. The rest might be even "Snipping Tool" or "FireShot" for bigger pics.
EDIT: I found my own AFCAD and I think I moved the airport instead as the lakes had been alright for me (UTX Canada v2). The airport was misplaced and needed to be shifted south. The mentioned tools are remaining the same...
It should be a piece of a cake doing that without the need for Pro-functions of ADE.
I added a picture how my AFCAD looks in ADE (pimped with some objects) and a sceenshot showing the result.
EDIT: Don't forget deleting the old airport background. It's usually huge and likely lifts the lakes, too.
Have fun (and read the manual).