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It connects 3 - 4 main bodies of water, the lakes in the middle are a high spot compared to the oceans on either side.

In the absence of the canal, did these lakes naturally drain to the sea, or are they in some sort of natural "bowl" that is higher than sea level?

Very few lakes on the planted don't drain to the sea. They are usually salty, smelly water bodies that nobody wants to be around.

See the cross section

"Natural bowl higher than sea level" could be called a lake.