From the Editors of The Daily Cat
It's normal for a cat to be fascinated by water. Also, some cats are not comfortable sticking their heads into the bowl, so they prefer to dip in their paws. Once that behavior starts, it can become a habit.
It sounds to me as if your kitty is just very playful, or perhaps bored, and needs more appropriate outlets for her energy. Try to do at least two or three interactive play sessions with her during the day using a fishing pole toy. You can also create some diversions for her to engage in when you are gone so she will not be so inclined to play in her water. Try leaving a few open paper bags on their sides with toys inside. You can also create a cat tunnel by connecting some bags or boxes together.
Another wonderful way for a kitty to spend time is watching a cat-interest video or DVD (try your local pet store or visit the Video Catnip website or the CatTV website). You can then follow television time with a play session. I think if you just do a few play sessions with her every day, she'll start to depend on those as her source of stimulation instead of pawing the water. In the meantime, use a placemat with a raised edge around it or a plastic cafeteria tray to protect the floor under the water bowl.