He's just trying to bury his water...it's completely normal. Though our Sunny girl doesn't try to cover her water, she does scratch the floor to uncover it EVERY time she goes to drink. It's hilarious...and adorable!!
Kitties bury their food, water, and anything that would land in their litterbox to cover their scent tracks. It's a bit of a prey type activity, but kitties are a bit of both, predator and prey. They're build like a predator, and eat like a predator...but they're still small, and still are prey for some animals, so they feel the need to cover their scent. If you think about it, though, it works both ways...they could also cover their scent for other reasons...to keep their prey from smelling them being near.
Anyway, there ya go...the reason behind it.