Deep water

some people use marine grease around the lid to keep water out.
silicon would work, probley be a b!tch to take off and clean the fliter tho.

there is a run off tube on the bottom of the air box did you plug it?

Also make sure all your clamps are tight. I had to use Marine grease on the Air intake tube to get a proper seal.

there is a rubber piece that connects the airbox to the tube, well on the inside of the airbox put silicon all around the intake tube

Make sure and check all 4 hoses that run in your air box. There is a drain plug, snorkel hose, carburetor hose, and then another breather for your motor....Im not sure what it does but I know it's pretty important!

It allows the engine to breath,let out pressure.Without it you'd blow a seal somewhere and lose oil.It would also push oil past the piston and burn oil.

The crank case vent below your air filter is very low in the air box. If you get enough water in the air box to reach the crank case vent, water shoots straight into your motor, turning your oil into mayonnaise! For a little added insurance against water entering the engine, I removed the factory crank case hose and bought 2 feet of the same diameter hose and routed it from my air box, over the carb intake tube and back down to the engine. This will allow the air box to fill well past the crank case vent opening without dumping water into your engine.