Running rough

Hey guys. Haven’t used my 2016 XMR 1000 a lot. 72 miles. However I was riding this weekend and went through some water. Maybe two feet deep. Ran fine for the next hour or so but then was. Bit hard to start twice and now running poorly. I would say sputtering. Starts but sputters badly at about 2000 RPMs and above. Looked in air box. No water. Thoughts and or suggestions? Thx.