as posguy said, some gets pushed out as crap sits on top of cover. Also, small leaks in the cover can let water slowly trickle through, becoming water on top of cover.
Many people will put the water on top into the pool, once it's clean of debris-
I use the pillows to keep the cover up (really to keep the wife happy, she thinks we need them), so don't have the same issues; instead, my pillows sink and are a pain to get out until the water warms!

Of course, when I first read the topic, I was about to say " It hibernates below your house and comes out when the woodchuck says its safe!"