Can you watch my stuff (laptop) until I get back. I have to go to the bathroom. It's usually a good idea to tell the person either how long you will be away of tell them specifically what you will go and do so that they can guess how long you will be gone.

A better expression would be the idiom 'keep an eye on'. After all, your deskmate doesn't really need to 'look after' your laptop - all they need to do is stay where they are so that nobody interferes with it or steals it. "Could you keep an eye on my laptop for a few minutes? I need to go to the bathroom.'

Your sentence is fine and conveys your intended meaning clearly. There are other ways to say the same thing as others have suggested. "a while' is pretty vague so you might want to be more specific when making such a request.