In June this year, I was crossing a stream that was flowing MUCH higher than it usually does due to crazy amounts of rain. My bike got pulled out from under me and was taken downstream. I had to run through the stream to catch the bike...so it was completely submerged for a little bit.
When I ride that particular trail, I use my wet/mud wheelset which has cheap Joytech hubs that came stock on the bike...to this day, I haven't touched the front hub and it still runs smooth but I have rebuilt the rear hub twice and the freehub is next to death. I have swapped the crankset on the bike but when it happened, I was running a square-taper setup and the bottom brackets I was using are only $20CDN so I just ran it until it made noise (which was basically right when I swapped the cranks in September).
I don't know about your bottom bracket setup (if you run cheap stuff you could pick up a spare and keep it on hand) but you may want to check the hubs as preventative maintenance.