What kind of boots? All leather or leather and cordura? Welted sole or glued sole? Claimed waterproof from the factory (good place to start)?

If you are in serious water without rubber boots, you might consider neoprene socks over your boot socks. Works for duck hunters, but you may need to size your boots accordingly. If you are buying new boots, I'd look at Danner, Filson, White, maybe something from L.L. Bean. You might also look at Nikwax products for waterproofing.