Water & Mud in Airbox then Overheated

2016 CanAm Commander Max limited 1000
I went riding on Saturday and we ended up going through quite a few mud holes. I got home, parked the Commander til the next day. The next day I drove about 3-4 miles and overheated. When I looked in the airbox the filter was packed with mud and water as was the front of the radiator. Rookie move I guess not checking the air filter box from the previous ride.
I cleaned out the box as best as I could but I’m worried about the water/mud that got into the clean air intake hose.
Any suggestions? Last thing I want to do is ruin the engine.
Thanks guys..