Wet highway puddle problem

Hi professors, When I'm traveling long distance on the highway and I hit a puddle I notice my TJ I6 looses power and slowly regains power and gets back up to speed in a matter of (I thinnk) several seconds. I say "I think" because I haven't traveled for a few years but am planning a trip soon. The first thing I thought of was the generator needed a cowl but it seem well protected. What may be causing this puddle power loss? Thanks, Steve