Hi For Eyes,
You may have read this already but there is more about the pros and cons of different types of mattress protectors in post #89 here.
Some of them do use more natural materials or fibers than others (such as cotton or wool) but I don’t know of any safety or “health” issues with any of them in terms of harmful substances or VOC’s.
If you are looking for “waterproof” instead of just “water resistant” then one of the protectors with a polyurethane membrane would be your most likely choice.
Phoenix