Can anyone guess what this small hole filled with water, in the center of a fort built in the 1600s on an island just off the coast of Colombia was used for?

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Based on hint 2 I'd say the level would rise when ships enter the bay. 

But for that, the fort has to be close to a bay. 

I can also see it being used for waterboarding of some sort.

Oh, wait.... No... It's messenger fish. Like pigeons, but the fish.
Right?

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In my limited knowledge of that area, most of the forts were built to protect ports, that were often built in places that had some natural shelter. That's why I thought bay. Could be any indent on the coastline, to be honest. Might be my limited English vocabulary.

I did say it was built on an island, in the Caribbean Sea, so not a bay exactly but… 😉