Ships crossing the Isthmus of Panama are raised high above sea level by a series of locks, and then lowered back. Rainwater refreshes Gatun Lake. In fact, a good part of the passage is through the lake itself. It would be possible to dig a sea level canal through Nicaragua, but it would be considerably longer.
Now we get to the real mystery:
Why the Caribbean entrance at Colón is to the west of the Pacific entrance at Panama City.
Build a pipeline that will use ocean water.