High water into intake, loud knocking

I have a 96 buick regal 120000 miles, 3.1 v6. I went through an intersection with high water, and a vehicle coming the other way pushed a lot of water over my hood. Car stalled immediately, when I got it home I pulled off the air intake, and the trap was completely full of water. I took it off and let it sit for a day, when dry I restarted the car and now there is a very loud knocking from the top end of the engine. I am quite mechanically inclined and can change or repair almost anything mechanical, I am just trying to find a starting point. If it may be something major like a piston problem or connecting rod I will probably have to take it in. Thanks for any help.
Rodney Moen