You can either just put the mouse in the water, or you can put the mouse in a baggie and then in the water.
By the way, I'VE never put a mouse in the microwave. I've just read that it can be done, with the risk of mice blowing up.
I don't know if you guys have heard of this, but there's also an "urban legend" of an old lady who stuck her weiner dog into the microwave to dry it off and the dog exploded. True or not, I'm not putting mice into the microwave after that story.