Brother had my '05 400 Sportsman in about 2+ feet of water, muffler was under water. Next day the battery is dead. He said he never shut it off when the muffler was submergered. And it done run later that day. Air filter is dry and no water in air box. Could the dead battery be related to the swamping, no alternator listed on parts pdf. is it part of the starter?

 

I would just charge battery and take it from there

sounds like something shorted under water so if battery now keeps charge then all is well

if not use a multimeter to find the guilty part