I bought a couple nice roll top dry bags with quick releases from Dick's Sporting Goods. Pretty similar to a duffel bag. They have a 55 liter bag made by Quest for forty bucks. That's a little smaller than an standard military issue duffel bag, which I think runs about 80 liters. I used one of their dry bags on a cross country trip a few years back, and it worked well. It doesn't have backpack straps though, so if that's a critical feature you're looking for, the Quest bag won't do the trick.
They also sell Yeti waterproof duffel bags, but like all Yeti products, they are stupid-expensive; their 100 liter Yeti duffel is 400 bucks.