I've never spent any time in the panhandle of Florida so I can't help much. If anybody else has any ideas for BruceWayne, please jump in here and offer up some help.
I was at a meeting where a couple of scientists were doing a presentation about surveys done in Saint Joseph Bay where there is an aquatic preserve. I know that's 100 miles away from Destin, but then I drive 300 miles to snorkel in the Florida Keys.
I would think that with all the barrier islands and back bays that there should be some worthwhile snorkeling in the area.