If you got a calm body of water, I prefer to 'walk' the pack across if it looks wadeable. Its significantly easier and fast than swimming. Make sure you undo the chest and waist straps though and put the shoulder straps on the loosest possible setting. That way you can easily 'slip out' if it gets too deep. Then just grab your pack and swim it across, use it as a float and kick with your legs. Thats how we got taught in the army at least. Ah and NEVER wear your boots when swimming. Makes life a lot harder! Gotten across New River Lagoon that way before and it works fine.

- Walking pack across New River Lagoon
If you are talking a river, then I would probably cross solo and then try and pull the packs on ropes as described before. Seems much saver as the current is usually significantly stronger than it looks from the side!
In terms of waterproofing, I use large pack liners ( i think they are sea to summit) with the big roll-tops. They work extremely well - you can even submerge them to quite some depth if you rolled them 3 or more times at the top. I tend to have one really big one as a general pack liner and then several small ones for other items (one for clothes, one for tent/sleeping bag, one for food etc.) Never had anything get wet so far.