1999 Toyota Corolla Question: Studdering Corolla

Went through large rain puddle sin the road. Drove fine for a while after. Son took the vehicle later, refueled it than startted having studdering/vibrations during acceloration with a definate lack of power. I met him and drove the car home, found the lack of speed but was able to get and maintain highway speeds. This morning I undid the gas cap initially after review of engine compartment components and started the vehicle. No problems and ran it to the store operating normally, 10 minutes later it acted up again... There was also a popping sound when increased engine speed coming from the air cleaner. Water damage?? bad gas?? SOS