I would, unless there is something unusual about the water - say, alligators, pirahnas, lots of leeches - not bother with waterproof anything. I'd get a second set of shoes to wear through stretches of water, take off the socks and hiking shoes, wade, put them back on at the other side of the water crossing.

Yeah, a nuisance if there are frequent water crossings.

The other option - just use shoes that fit. Blisters take three things to form - friction, heat, and moisture. If my shoes fit well I don't get blisters even when the other two exist. I have gone on a hike with 10+ water crossings wearing wool socks, non goretex hikers, and waded all the crossings. Most of the water leaves the shoe, unlike goretex shoes, and my wool socks (lightweight) were damp but not uncomfortable. No blisters.

What one needs at the end of the hike is dry socks, tho. Trench foot can set in if your feet are always wet.