when shooting on the beach/reef with a tripod I stick duck tape on the lens hood then throw a towel/sarong over the lens and body and tape the front to the hood to stop the wind blowing it over the lens. The towel comes in handy to get a view through the viewfinder, if you stick it over your head, when the light is intense. Also comes in hady to wipe off your camera gear and perspiration.
I used to swim out over the lakey peak lagoon in Sumbawa, park up on the reef shoot surfers all day and swim home, no worries. Did it for about 6 months with a 10d and 100-400. Here's a few from a hard day at the office...
I've never had problems with sand, I always keep a pelicase nearby (the small ones on a piece of rope make a great tripod weight) and never change lenses in the field, common sense really.