Last year was a rough one for Cozumel. On July
18, Hurricane Emily blew gusts over 150 mph. Then
on Oct 19, Hurricane Wilma, at one point the most
intense Atlantic storm in recorded history, pounded and
drenched the island for days.
While many hotels and homes were seriously damaged,
  topside the island has bounced back like a champ. All but
  a few resorts are open and in good condition. A number
  have taken the hurricane opportunity to renovate and
  look better than ever. However, El Presidente, one of the
  hardest hit, has just begun rebuilding and Sol Cabañas
  del Caribe may never reopen. Some shops downtown have
  closed permanently, but the good cantinas still serve up
  tasty meals and potent margaritas.  
Nearly every diver pick up pier was destroyed or damaged but they’re nearly all operational now. I stopped in
about 20 shops of the nearly 90 dive operations on the
island and business was slow. Several, including two bigname
operations, told me I could have a boat to myself
the following day.
Many small dive operations are struggling, as Dean
  Knudson (Golden Valley, MN) reports of Pacual’s Scuba
  Center. “His boat was flipped upside down and sunk.
  Both engines were submerged. He lost his gauges, most
  weights, and his Bimini top. In February the boat was
  functional; it had been painted, the fiberglass was new,
  though he still does not have gauges. Pascual asked us to
  take a taxi each day to the Caleta Marina, instead of meeting
  us with the boat at our condominium. This was annoying,
  but understandable, given his fragile financial condition. It would save him money on gas, a major expense.
One day the boat was crowded with 10 divers. It was difficult
to fault him for booking so many, as he had had little
to no business since the hurricane and was struggling
financially. He managed to lead an interesting dive, even
for the more experienced participants.”
Contrary to what some people who make their money
  off divers say, there is no debate that the underwater
  environment has been significantly
  rearranged forever.
  Even to a 32- year Cozumel
  veteran, many of the 20 or so
  sites I surveyed in February
  were unrecognizable.  
  
    | “. . . the underwater environmenthas been significantly rearranged
 and changed forever.”
 | 
Shallower sites bore
  the brunt of the damage,
  and some are covered with sand or badly denuded. Bill
  Allen (Melbourne Beach, FL) found in February that
  “Tormentos and Paradise are now effectively buried under
  sand, sometimes feet of sand. Santa Rosa and Punta Sur
  (deeper reefs) have a good dusting of sand. The underwater
  scene recovery is already taking place. When the
  current is running, you can watch the sand being blown
  off the reef structure. Cozumel has changed, and it’s not
  all bad. It is all new.”  
The more delicate life, such as long tube sponges; sea
  fans, bushes, and rods; finger, pencil, and thin lettuce leaf
  corals; and leaved algae were all but obliterated. Hardier
  growth such as sheet, boulder, brain and star corals and low profile branching tube, elephant ear, and encrusting
sponges, have fared better. However, silt may yet choke
existing sponges, and corals that are not easily cleansed
by the current. While some readers report fish life is as
good as ever, others don’t see it that way. Surveys by volunteer
divers from REEF show a reduction in numbers of
many species, especially the sand dwellers
I was especially upset at San Juan up north and Dalila
  in the mid south. San Juan provided
  its customary high-speed
  ride, but hawksbills and freeswimming
  eels were nowhere to
  be seen (though I did see two
  monsters below overhangs), nor
  were the verdant gardens of watercress,
  hanging vine and other
  leafy algae. Piles of broken finger
  coral littered its expanse. Oddly, it even sounded different
  — quieter. Dalila, once a rolling plain of coral and
  Gorgonians, looked more like a lunar landscape than a
dive site. 
On the brighter side, the storms revealed and created
  delightful new chasms, caverns, and swim-throughs.
  At Punta Francesa, Columbia Deep, and Palancar Bricks
  I could stay inside one or another of these tunnels for
  much of the dive. Moreover, close inspection revealed
  new life: tiny sprigs of fresh finger coral and sea fan here,
  a pregnant Sargassum triggerfish and silver-dollar-sized
  peacock flounder there,
 Some mid-depth sites such as Palancar Bricks and the
  upper reaches of the Santa Rosa Wall, although silted, are
  better preserved. At the former site, the hurricane uncovered
  many unusually shaped bricks said to be from a load
  that went down in transit from the mainland. The bricks
  appeared to have been arranged by divers, but nonetheless
  added an interesting aspect to the dive.  
Not surprisingly, the more southerly deep reefs survived
  better. Maracaibo Deep, which takes the diver below
  recreational limits, continues to exhibit handsome arrays
  of sea fans, rods, bushes, and healthy tube sponge. I spotted
  two juvenile nurse sharks — my only shark sightings.
  Bill Allen of Melbourne, Florida, also noted a paucity of
  fish in February: “Noticeable by their absence are the
  large green eels and large grouper. I saw only one green
  moray and maybe a half dozen medium-sized grouper.”  
The Devil’s Throat, entered at ~90' and exited at
  ~125', remains open, though the walls were scoured by
  sand. Finning north to the Cathedral, you’ll find that the
  landmark cross-shaped sponge on the ceiling has been
  torn away save for a nubbin.  
There is still scuba to enjoy. To access outstanding
  deeper sites such as Garganta del Diablo with its
  northward add-ons, Maracaibo Deep, and the Wall of
  the Widows, Maya Gate/Labyrinth, and Devil’s Other End trio, only the rare gas sipper will be able to safely
and comfortably descend on a standard 80 cu ft. tank.
Choose an operation such as Liquid Blue, Aldora, Living
Underwater, or Deep Exposure. They have thorough
knowledge of the reefs, tanks that provide an opportunity
to dive deep for extended times, and a willingness to visit
more advanced sites for better post-Wilma diving.
If you don’t pick the better dive operations, you can
  be in for trouble. In January, one of our readers went out
  with a cattle boat and reports: “The first day our captain
  took a while to find us drifting because he was too busy
  fishing. The second day we had to endure him vomiting
  from a hang over. The third day he left us drifting at sea
  for 45 minutes. Finally after kicking 1.5 miles, we reached
  another dive boat . . . Blue Bubbles never offered an apology
  — only a new captain the next day. They felt it was
  not a big deal. Drifting in a 6-knot current for 45 minutes
  in 3,000 feet of water is a big deal!”  
Marjorie Griffing (Shoreview, MN) went out with
  Dive Paradise in February. “During the morning dives,
  the operation did a good job of grouping divers of like
  experience. In the afternoon, however, there was no
  attempt at grouping people appropriately. They sent out as few boats with as many people as possible. While we
enjoyed looking at the fish doing their own thing, other
divers seemed to enjoy swimming headlong into a school
of fish on purpose to scatter them. I suspect they lit bugs
on fire with a magnifying glass as kids! One afternoon, we
objected to diving Villa Blanca wall again and it seemed
they punished us. They dropped us over sand with virtually
nothing to see. It was at least four minutes into the
dive before we saw anything living.”
But, our favorite operations always seem to get good
  comments.  
In December, Wayne Whittier (New Braunfels, TX)
  went out with Liquid Blue Divers owned by Roberto and
  Michaela. “Their attention to detail is first class; rinsing
  and cleaning your gear nightly, towels and jackets on
  the boat, intervals at a beach restaurant, and providing
  120cf steel tanks that allow longer bottom times at greater
  depths. We were always the first boat to the dive site each
  morning, giving Roberto the opportunity to point out
  many creature sightings that would hide once all the
  other boats would arrive.”  
And, in November, Peter and Sandy Oemichen (Oregon, WI) said that “Deep Blue did a fine job of
accommodating divers under less than ideal circumstances,
providing transportation, and handling our gear.
They were eager to please. (The captain even took my
suggestion to approach divers with the motors downwind
so divers waiting to board didn’t have to breathe exhaust
fumes). Our last day, we dove with Living Underwater
and Jeremy Anschel. I was impressed with his new steel
tanks and the service.”
Tom Day, there in March, said “my heart continued to
  sink on dive after dive seeing how the reefs were scrubbed
  of their corals. It also looks like a fresh layer of snow has
  fallen on most of the reefs. Tuniche was scrubbed, but
  along the wall fared better, deeper down 80-100 there
  were still corals and sponges and lots of large grouper,
  and sharks, and I saw a large mating pair of puffer fish. Barracuda . . . current was as fast as I have seen in 15
years. San Juan the same. Tuniche had upwellings along
the wall except one large pass that usually has a downwelling.
Barracuda had its typical downwellings . . . Aldora
Divers was fantastic, can-do-will-do attitude, groups of
like experience together, top notch office and dive staff.
Equipment repair? Done! Dive site request? Done!”
So, pick the right dive operators, keep your expectations
  in line, and go have a dive and a cold cerveza.
  Cozumel is still a lot of fun. But don’t expect to find any
  bargains. Prices at hotels, dive ops and eateries were much
  as they were on my pre-Wilma trip.
– Doc Vikingo
Aldora Divers, www.aldoradivers.com
Deep Exposure: www.deepexposuredivecenter.com
Liquid Blue Divers, www.liquidbluedivers.com