Today there are basically two companies offering water taxi transport from Chetumal to San Pedro and vice versa. You can drop the price a bit if you bargain, their offices in Chetumal are next door to each other directly at the portīs entrance. One of them is more comfy, the other one will be a bit cheaper in the end. You decide. Keep one thing in mind: if possible try to sit as far in the back of the boat as possible. The trip will be quite rough especially in the front.
Reservations: you can do that online, but when we have been there there were only a handful of other travellers, so there is no need to. But I donīt know if that changes depending the season.
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http://www.tripumdiewelt.de/2011/07/reif-fuer-die-insel.htmlcheers
biene and Holger