Spits, Sputters then keeps going

Hey Guys,
 I like to ride the South Canadian River. If you've never ridden it, it is simply MILES of sand and river crossings. One of my favorite trips was an overnight trip that started from just below the Holdenville,Ok Lake Dam and we rode 61 miles down river until we ran smack in to Eufaula Lake. Camped for the night and then rode back the next day.If you've never ridden the South Canadian, make it a point to make it there some day.
 Anyway, my 05 Kodiak 450 has ridden this river for the past 4 years with no problems. However, lately every time I cross the river (about 18-24 inches deep) or hit ANY kind of puddle, my Kodiak will spit and sputter and cut out on me. It doesn't die, it just sputters for a few seconds and then keeps going.
 On the other hand, I did hit a huge mudhole pretty hard during a race and it took about 60-90 seconds before it would stop sputtering and keep going (needless to say it cost me the race).
 So, anybody got any ideas why this is happening and what it would take to fix it?

'preciate your help,
James