We took a day trip to Mantanani. There are two ways to get there now, but our tour took us on a 1 hr 45 min drive north, followed by a 30-40 minute boat ride to the island. There was some waiting time between as we collected snorkeling gear and life vests.
The island itself, once you get there, is quite nice. As of February 2014 there is a lot of construction going on to add more bungalows, but it is still quite desolate compared to the other islands. There was a large group of people who went, but due to time constraints of squeezing in two snorkeling sessions plus lunch, there was no one swimming on the far ends of the islands. It actually felt like a desolate, tropical paradise. The beaches were a nice white sand and the water was clean and very calm on the side facing Borneo. We could even see Mount Kinabalu from the beach.
That said, if you can book a trip that stays on the island overnight I would recommend it. We needed to wait about 45 minutes after landing before taking the first snorkeling trip, and between that, lunch and needing to be back at the boat by 4 made us feel that we were on the clock a bit too much. We all wanted to stay longer.
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