Here is a list of gemstones that are TOXIC in water and should NOT be used directly in gem elixirs etc.
Actinolite
Adamite
Ajoite
Alexandrite
Amazonite
Atacamite
Aquamarine
Auricalcite
Azurite
Beryl Group:
-Bixbite
-Emerald
-Aquamarine
-Goshenite
-Heliodor
-Morganite
Black Tourmaline
Boji-stones
Bronchantite
Cavansite
Celestite
Chalcantite
Chalcopyrite
Chrysocolla
Cinnabar
Conicalcite
Copper
Covellite
Cuprite
Dioptase
Dumortierite
Emerald
Fluorite
Garnet
Gem Silica
Galena
Garnierite (aka Falcondoite)
Hematite will rust, but not toxic
Iolite
Kunzite
Labradorite
Lapis Lazuli
Lepidolite
Magnetite will rust, but not toxic
Malachite
Markasite
Mohawkite
Moldavite
Moonstone
Morganite
Pietersite
Prehnite
Psiomelan
Pyrite
Realgar
Ruby
Sapphire
Selenite (Although not toxic, friable; tiny shards may break off in water)
Serpentine
Smithsonite
Sodalite
Spinel
Spodumene (aka Kunzite)
Staurolite
Stibnite
Stilbite
Sugilite
Sulfur
Sunstone
Tanzanite
Tiger Eye
Topaz
Torbenite
Tourmaline
Tremolite
Turquoise
Vanadinite
Variscite
Vesuvianite
Wavellite
Wulfenite
Zircon
Zoisite