While replacing the van's carpet I noticed there're a few holes in the floor that started to rust around edges. There's no isolation or any protection between the floor and the ground, you can see straight through them.
What's a good way to patch those? Would be great if the solution both stopped the existing rust to spread and also prevented water coming in going forward.
Cars and vans tend to have holes left in the body after the production process, and these are usually filled in with rubber grommits. It could be that your van is missing one of these, or as Mark mentioned in the comment on your question, it could be missing something like a screw (or something used to be screwed in there).
As there is rust, your best bet is to sand this down to the bare metal and maybe use some rust converter on the affected area. You could then fill the hole in with filler, at which point you could then spray paint over it with primer and a top coat.
I would investigate though whether or not this hole was meant to have something in it like a grommit or screw before you start filling it in though.
There are two routes I'm aware of you could take.
First, you could weld the hole shut. You'd need to clean the area of rust/corrosion with a sander, then get a small circular punch out of the same size (diameter/thickness) of metal as the hole, hold it in place, tack weld it, then finish weld it, then paint match it to keep rust at bay. (General description of the process.)
If aesthetics are not an issue (going to be covered by carpet, never to be seen) and/or you don't have access to a welder, you could try using fiberglass sheeting and rust converter.
I bought my son a Jeep Cherokee where the floor at the driver's seat was riddled with rust holes. Nothing big (mostly pinholes) and nothing structural. I cleaned up the area the best I could, then took some fiberglass sheeting and cut some to size. I applied some POR-15 (this is what I used ... any rust converter should do the same job) to the metal, then stuck the fiberglass to it, then painted over the fiberglass. I did this from the bottom side. Once dried, the coating provided an air/water tight seal. It also becomes as hard as a rock. You can do this to both sides if you like, but the bottom side is sufficient for it to work. If you do go this route, be aware the POR-15 will stick to everything and won't want to come off. Any paint brush you use will be ruined. It will also bond two pieces of metal together, so once you've gotten it on the sides of the can as you are trying to dish it out, the lid will bond to the body of the can, which means you'll never get it open again. The stuff coats very well, so even a small can would be enough to do just the single hole you're showing in the picture, or even many small holes (if that's what you've got going).
