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We haven't done the ocean rafting but have done the GBR on a different cruiseline.
They take you out to the outer reef, about 1 1/2 hours away directly from the ship, the reef is much nicer than the inner reef and they have a large pontoon out there. On the pontoon is normally a downstairs viewing area of the reef, an upstairs viewing area with a slide into the water, you can snorkle (or scuba if arranged). Or just swim, they have wetsuits and all the gear along with pool noodles and floatation devices and vests. They also have a roped area with boys to help people move around a part of the reef. Lunch is served bistro style and there are drinks as well as ones that can be purchased. Our pontoon also had a submarine so people could view the reef further away.