I've typically just taken plastic shopping bags and wrapped them around the shoe, cut out the hole for the cleat and then duct taped over the whole thing to help it hold its shape and for helping them last more than one usage as well. I add some velcro to the back so I can put them on and take them off easily enough.

After watching the video below I want to see if I can find some socks big enough and try this idea for waterproof socks. I wear sized 13 shoes so that might be a real problem.

https://www.youtube.com/watch?v=WRCXy_UHPVc

I figure cut out the hole for the cleat and then you should be able to fairly easily put the sock on and take it back off. I think I would have to do it part way up the leg as well to help keep the full area up around the top of the shoe dry. Naturally I would do both the bottom of shoe and the top of the shoe as well. Dirt cheap way of having the waterproofness that you can take off so your feet don't want to bake when it's not raining.