oh no not water in the exhaust you have to buy a new ski immediately,,,, JUST KIDDING it is called a water box, actually no water in it will burn holes in your exhaust hoses. it's normal !
Your yamaha has a wet exhaust. The exhaust pipe has a water jacket inside and it the water mixes with the exhaust gas at the end of the pipe. The water cools the exhaust hoses so they dont burn up and split. the standing water is normal in the waterbox ( muffler if you will) It wont hurt anything. When you pull it out of the water start it up and give it a few quick revs. that will blow the water out of the exhaust. Not all of it but most of it
Rob