The visit to the natural pools/coral reefs is definitely the best ecotour in the region. During morning lower sea tide, natural pools, isolated from open ocean, form for a couple of hours.
The place is only accessible by locals' rafts, called "jangadas". These "jangadeiros" can be contacted directly in the shores where the rafts leave (most of the nearby beaches, such as Milagres, Camaragibe, Marceneiro and Toque have rafts), but hotels and inns have good and handy contacts with several of them.
There are a handful of different pool palces, but the most famous ones are located at the Toque beach.
The isolated pools have crystaline water, ~3m of depth in the deepest parts and several fish and coral species. Since the isolation of the pool from open ocean is a crucial part of it, tours happen in the morning only. Try to leave 9:30am at maximum, so you can enjoy at least 2 hours of it.
And definitely take snorkels and goggles if you can - some "jangadeiros" rent it, but not all of them. Also, any form of diving shoes or protective rubber shoes is very helpful when moving around the reefs - urchins (ouriços) are everywhere and can hurt your feet.
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