As the world's second largest reef formation - over 600 miles in length - lies off the coast of Quintana Roo and Belize, snorkeling or diving shouldn't be missed when you visit.
I'd love to have diving recommendations to share here. I simply snorkel, so am reporting on what I myself have tried.
Cozumel
Beach club snorkeling
First experience : caught a taxi from town down towards the southern end to a beach club. As is often the case, entry is a simple matter of buying something to eat or drink. Chose this place because we'd read you can "drift snorkel" right offshore. No boat outing required. Tried it, enjoyed the snorkeling briefly, but certainly did drift. Not wearing flippers, had a real struggle against the current once I'd drifted far enough. Finally made my way to shallow enough water to walk back. Tiring, a bit worrying, and convinced me that a boat tour to snorkel is a nice idea.
Snorkel tours from the ferry pier
Second experience : booking a snorkeling tour right from the ferry pier. It was great, so that I've gone back with a second friend. You'll be taken to two or three spots to snorkel; they say three, but both times it was two spots, with the guides explaining that there were jellyfish in the deeper waters. Who knows. It didn't matter. The two spots were fabulous both times. Deep water, lots of fish. Often possible to swim without fins or life jackets, if you like (as I do). Plenty of fish, many attracted by food the guides are tossing in, so not purely natural, but gorgeous to experience anyway. Top choice if you don't mind the logistics and expense of getting to Cozumel
The organizers on the pier will tell you you're going to be on a boat going out right away, if that's what you want to hear, but it doesn't mean anything. So be cautious if you have a schedule that must be kept. And note that you can bargain on the price; it's not hard to get a reduction from what's first quoted. Use the savings for or toward your tips for the captain and guide.
Getting there :
ADO bus, colectivo ('combi') minivan or taxi to Playa del Carmen. Ferry to Cozumel. Snorkeling tours from the pier you arrive on. Buy your ferry ticket one-way only if there are still two companies alternating service, so you'll feel free to take the first available ferry when you're ready to return.
Many of us keep looking for a ferry or any boat service to Cozumel from Cancun, but there is none. There are some old ads around that will get your hopes up.
Puerto Morelos
At Puerto Morelos, the reef is so close to shore that you can see it a reasonable swim away. However, you're warned not to swim out on your own, because you could get cut up by one of the little motorboats operating tours. The official operation is right by the town square and pier. They give a great tour. Walking up the beach you'll likely be solicited by others who will offer to take you out; be sure they provide wrist bands showing a fee has been paid to the official coop. You'll snorkel in two different locations, one they'll tell you is for seeing coral, the other for fish. As you can guess, you see coral and fish wherever you snorkel, and the variety is wonderful.
Since the reef is so close, you're snorkeling within minutes, another plus to Puerto Morelos. On the downside, the water is so shallow that it's very hard to avoid touching something. And you must try your best. The reef is harmed by contact. Of course, the coral can cut you as well - you never want to touch anything. And there can be dangerous things on the sea floor, so you wouldn't want to let any bare part of your foot touch. If, when you wish to rest a bit, adjust your mask, etc., you roll onto your back, you can lift your legs and keep away from things. But I saw many men dragging their flippers along the bottom, keeping themselves upright as if standing on shore, rather than watching where their feet were going. While all the boat captains and guides were attentive to their tourists, my impression was that the ones who leave from the town pier pay more attention to protecting the reef, and instructing snorkelers on what not to do. But they were all good tours.
Getting there :
Puerto Morelos is only 26 km (15-16 miles) south of Cancun's airport. You can take a bus from the airport on arrival. But if you're already in Cancun, go to the ADO station. ADO buses as well as local colectivo ('combi') minivans offer frequent service. The combis charge 20 pesos (US$1.20) each way. Any bus will leave you at the highway overpass, by the 'colonia', not the port area. If you walk to the port, be wary of mosquitos, crocodiles, traffic and sun. Better to just take a taxi for another 60 pesos. Minivan bus service runs between the colonia and the port for 8 pesos, but the vans are often full by the time they stop at the federal highway. If you see a bus, Ruta 1 or Ruta 2 won't make any diffence when heading to the beach.
Isla Mujeres
The only snorkeling we've tried from Isla was offered by the people who corral you as you walk towards Playa Norte from the ferry pier. Almost immediately, there are kiosks and people on the sidewalk with picture signs of snorkeling tours. Would not recommend them, would not go out with them again. They say you'll snorkel in three locations, which sounds great, like Cozumel. But you go in the water once, and then they say you've seen three things. After that, the boat went on south to a little restaurant where we were let off, to wait if we chose, while others went on to the underwater sculpture garden, as they'd paid more. Photos of that hadn't made us think we wanted to snorkel there, so we walked to the turtle sanctuary, toured it, and started walking back towards town, till we caught a ride on a golf cart. I conclude that snorkeling from the southern beach clubs or park might be the best idea, but can't say until I try. In the meantime, I enjoy just swimming from Playa Central (which last year I took to be part of Playa Norte). The water is lovely.
Getting there : Ferries run from Puerto Juarez on the north side of Cancun (2 locations), Punta Sam (even further north than Puerto Juarez, and the only car ferry) and the Hotel Zone. If you're staying in the hotel zone, of course the ferry there is more convenient, but I think going from the Ultramar terminal at Puerto Juarez is the best. You can get there by taxi (eventually you'd go up Bonampak to Lopez Portillo) or by combi (from the north side of the ADO station on Avenida Tulum, or along Tulum anywhere up to Crucero): look for white minivans with Puerto Juarez among the words written on the windshield. Show up any time, as the ferries run every half hour. Late afternoon and late night that changes to hourly each way. Be sure to check what the last departure will be for your return. The fare is cash only, 146 pesos, which in January 2016 is less than $9. The trip only takes 20 minutes. Deckhands will help get luggage on and off the boats; no charge for luggage, just tip. There are fellows with carts waiting on the pier who for whatever tip you'll give will help carry bags further along, not sure how far, but it seems a tip would get whatever you need. The lower deck has upholstered seats and air conditioning. The upper deck has sun or moon, water spray, and musicians who've never met a Simon Cowell.