It's been thirty years since I was in the Gulfport area, but back in the late 70s, the Air Force had a standing order that we were NOT allowed in the water within something like 25 miles either side of Biloxi. That was still fairly soon after Hurricane Camille, and they considered the water still too polluted to be safe. I wasn't a diver at the time (and still won't be for another couple of months), but the times I walked along the beaches in Biloxi and Gulfport, I thought the water looked pretty nasty - heavy amounts of suspended stuff, and an often unpleasant smell. Close to shore, at least, you couldn't see the bottom through more than about 6" of the water.
We did make a couple of weekend trips to Pensacola while I was stationed at Keesler AFB, and I have to agree that the water there looked incredibly better than the water in Mississippi. I'm sure a lot of things have changed in 30 years, but I still think I'd head to Florida if I wanted to get in the water, instead of diving around Gulfport or Biloxi.