06 polaris scrambler 500 problem running thru water.

I ran my 06 Polaris Scrambler 500 thru a few water holes while trail riding(all water depth was from the foot rests and lower). and noticed that when i came out of the water puddle, i had very little power. Let it sit a minute or 2 and it was fine. When i went at a slow crawl thru the water i had no problem. Just wondering if anyone has knowledge of y this could be happening?