Big puddle problem

Its been raining all day in NY today. Roads were flooded. I hit a deep puddle at about 60mph. I felt that the engine drank some water and check engine light started blinking and stayed on after that. After 5 mins the car was running fine but the light is still on. I wonder if it is just a cylinder misfire caused it to turn on? im going to autozone to check it out. Does the light stay on, even after the problem is gone, until the codes are erased?

I have a 1996 Passat VR6 GLX, 109,000 miles.

And can anything else be damaged if i hit a puddle at that speed? I dont know much about cars, but i just wonder if anything else could have gone wrong because the puddle was very deep and I almost stopped after i ran into it and the car almost went out of control.

It was what I thought it was. Multiple cylinder misfire. after the codes were erased, the light did not come back on