That was me a few years ago. Can be fixed with £500 of new engine, no biggie really.
CAIs are stupid for this reason though. No other cars struggle with that amount of water, but searching for that extra .5bhp leaves you with a POS pipe that sucks up conrod bending amounts of water in as little as 6" of water. So not worth it on a road car.
After that, with a new engine in it, I got myself a stock airbox and never worried about it happening again.