I use a shallow clear rubbermade box (under the bed type) for the puppies. They cannot get out, but mom has no problem stepping over the sides. I start out in the pack and play which I have modified to have an opening in one end for mom to come and go. That way I can put mom's food and water in the end of the pack & play for those first days when she does not want to leave the pups. Later, she can come on out when she needs to.
Then I move them to the play yard, putting the clear rubbermade box in one end, plenty of pee pads around and an area for the food and water. Since the puppies cannot get out of the box, I don't worry about them getting into the food and water. When they get big enough to get out of the box, I do away with it and use a large doggy bed in the one end -- big enough for mom and all puppies. Then I am letting mom out a lot and her food and water goes outside of the puppies play yard. I give them some toys to play with and make sure to keep all of the area lined with pee pads. Makes cleaning up a breeze. Three of the large sized pee pads just fit in the play yard and you can just replace them once or twice a day, depending on how messy they are. By 4 weeks, the puppies are getting their own food and water. I like to use the big stainless steel puppy feeder that has a raised are in the center. That way they can all get around it comfortably. They still walk in it and occasionally even leave a present that has to be thrown out with all the food.
But what can you do? I like the water bottle that I am now using. I too, worried over the water bowls. They were always playing in them, making a mess, dirting the water, etc. So, now I have the water bottle on the side of a crate. They all learn to use it in no time. Had to put the small crate in to hold the water bottle as I could not get it to stay on the play yard side. But I made that the new bed area (be sure to take off the door). So they still have plenty of room.