I did that to my CR250 once as well, but the water was pretty deep. Honestly, I don't think any amount of waterproofing would have prevented that mishap. Lots of kicking didn't get the bike running. We ended up pushing it up a hill to bump it, twice, before we finally got the fire lit again and kept it running. Mental note: don't attempt water crossings a few days after major flooding. ;)
But it did break in my new boots quite nicely. Apparently standing in knee-deep water for 15 minutes, while wrestling a dirt bike out of the mud at the bottom of the stream, works quite well as a break-in method. On the plus side, I didn't have to stand there and hold the bike as it stood up quite well on it's own. :)