polaris 700 engine noise need help

[jhendry]

I have a 2007 polaris sportsman 700 with low hours around 100 or under. Ive never rode it hard just trail riding. I recently got stupid and went playing in a small pond. the water never rose over the front and never stalled while in the water. Hours later i noticed some noise so while it was running i pulled the oil dipstick and water shot out. I took it home and drained the oil and trans fluid, replaced it along with air filter, one spark plug(right side). I just ran it and still I have this very loud knocking, progresses when rpm rise and a huge loss of power. Does anyone have any suggestions. Im pretty handy, contractor by trade, not saying i can rebuild an engine but If simple i can do it. I took off the engine cover on the right side and didnt see anything out of place, not much there other than 2 gears, large and small. no oil though, is that normal.

any help would be great.