I would take everything out of the bed to try and determine where the dust is getting in. From what I've seen, most of it comes in through the tailgate. You can try sealing the tailgate with strips of pipe insulation that you can get at a hardware store. Also look for drain holes near the forward part of the bed.
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Honestly, though, it's a tough battle to fight. Pickups just aren't made for sealing out dust, which is one of the reasons I like having an SUV. When I had my pickup I was constantly fighting this. One thing you can try is putting the stuff you'd like to stay "clean" (typically your sleeping bag and maybe whatever it is you sleep on - a sleeping mat or mattress or whatever) in a big, heavy duty plastic trash bag and sealing that up. Food should also be sealed up and as for everything else - well, as the Marines like to say "Embrace the suck" or in this case "Embrace the dust." :sombrero: