Drove through Puddle and now..UH OH

[stangboy35]

I have a 1999 GT Auto with 40K. Last night here is South Florida we had downpours and the streets were flooded. I had to drive home from the club and went through several large puddles..very slowly. They were about 3" deep.
Now today the engine makes a ticking / rattle noise when the engine goes above 3000rpms. Will this go away? Has this happened to anyone?
Thanks
ROB