It depends upon how deep the water was. Also if it was raining then the filter may get a little wet cause water gets in the engine bay from the side of the hood and travels down. So some may drip on the filter. That's ok. Just make sure the filter isn't submerged in water. That's when you can hydrolock your engine and kiss it goodbye.
Here's a link for the V6 Intake
http://6thgenaccord.com/forum/viewtopic.php?t=856