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,...
We were staying at São Miguel dos Milagres and we were intrigued with the natural pools tour. A guy came and picked us up at our inn, at about 8am; the tide was down, so we walked about 50m towars the coral reef, were his raft were waiting. He tooked us about 100-150m forward, were we could see the natural...
Going to São Miguel dos Milagres and not visit the natural swimming pools is like going to Paris and skip the Eiffel Tower! Likewise, sometimes it is a little bit crowded but if it isn't the peek season, it worths the visit. Best to go with the 'jangadeiros' since they know the tide.
I booked a tour from my hotel and the boat took us to the natural pools. It was an amazing experience to be so close to the nature. The water is really clear and full of sea animals. Make sure you don't step on the corals to preserve the environment.