In the past, gems were put directly in the water to prepare gemwater or "crystal elixirs" and therefore had to be cleaned regularly. Besides the cleaning issue, stones often also emit hazardous substances (e.g. bedrock). Those contaminations were consumed along with the water. Some healing crystals that can be used in external applications without a problem may even release toxic substances if they are placed directly in water.
The perfect way to avoid those issues in preparing gemwater is to use gem vials by VitaJuwel as the gems are sealed in the glass vial and infuse the water without having a direct physical contact.
Seriously, why would you want to put something you dug up from the earth put in your drinking water, when there's a much more hygienic way to prepare gemwater?