I wear NRS neoprene boots on canoe trips, and they are the only footwear I take with me (I don't like carrying extra weight around for "in camp" footwear vs. "travel" footwear. I get out of the boat early whenever possible to save wear and tear on the hull, I'm just careful not to overstep the height of the boot. However, the neoprene boots are not great relative to your instep or ankle support, so I put Cur Rex inserts in there.
The upside is your foot remains dry, and so do your pant legs because the pant legs bunch up on top of the boot (its a real fashion statement). Your feet also remain pretty warm. The downside is you sweat, so you absolutely create moisture in the boot. The socks are soaking when I take them off at night. My trips are generally 4 days long, I've never had a problem, but I could see how a funky fungus problem could result on a longer trip. At night, I wedge a couple of sticks inside the boots, to prevent them from collapsing on themselves and trapping moisture in there. They're still a bit wet on the inside in the morning, but at least I've given them some small opportunity to breathe.
I wear those same neoprene boots to snowblow the driveway, to tromp around the snow around the house (in snowshoes too), in the muck of spring, etc. Mine have a few years on them, and a pinhole has developed in the heel of one. I'm going to have to replace them (although I'd like to try a bicycle tire repair patch first...), and the NRS style now has those bungee shoelace things on them. I'm a little concerned about those getting hooked up on all kinds of stuff, but I guess we'll find out when I get around to replacing my existing ones. It is the primary reason I'm delaying replacing them - I like the velcro on the existing ones.