All crystals need cleansing, whether you wear them in your jewellery, have them sitting on your mantle, or use them for specific holistic purposes. Crystals pick up from their environment and can become 'clogged': a cleansed crystal will look and work much better. Here is a user's guide to crystal maintenance.
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Most crystals and gemstones, in jewelry or on their own, will pick up negative or unwanted energies over time. They are a bit like sponges absorbing and reacting to the environment's energies. The ones I know of that don't absorb energies and thus never need clearing are citrine, kyanite, azeztulite, and Super Seven.
Crystals and stones that are used for crystal healing should be cleared and cleansed of negative energy prior to any healing work. You will also find that clearing stones makes them more cheerful and positive to have around.
Here are a number of methods that are commonly used to clear and cleanse crystals and stones to restore their bright, happy, vibrant energy. Some are more complex or take longer, others are extremely simple and quick. Use whichever suits you and your crystals best.
Salt Water: While this is a popular way to cleanse crystals, I recommend using salt water very carefully, if at all. You need to know about your crystals to be sure that they are not porous or soft, so they won't be damaged by water. Salt water can get into the structure of some crystals and stones and cause them to break. Some stones that don't do well in salt water are calcite, carnelian, halite, hematite, labradorite/spectrolite, lepidolite, lodestone (magnetite), mica, moldavite, opal, turquoise, ulexite, clusters of most stones, and there are surely more. When you do use salt water, do so cautiously and don't leave your crystals in it longer than absolutely necessary
Sea Salt: Crystals can be placed in coarse sea salt for up to 24 hours to clear them. They can also be stored in sea salt to keep them from picking up energies from their surroundings. In humid areas, using sea salt can sometimes cause the same problems as salt water. It can also get stuck in the crevices of clusters and eventually combine with water in the air and split the cluster.
Sunlight or Moonlight: The rays of the sun and moon are energetically very clearing and cleansing, as well as energizing. Placing your stones outside where they can soak up the sunlight or moonlight for a day/night to a week is very beneficial. Do be careful though, as some the colors of some stones may fade in the sun. A few of the stones that will fade in the sun are amethyst, celestite, opal, and turquoise. If you have any doubts at all, be sure to use only moonlight cleansing.
Earth Burial: As creepy as it may sound to those of us who grew up watching horror movies, burying crystals and stones is very cleansing and healing to them. You can bury them in the Earth for 3 days to a week, either in your yard or in a flower pot. Be sure that if you bury your crystals in the yard that you mark the spot. You don't want to have to dig up half the yard to find your stones again
Smudging: Smudging is one of my favorite methods of clearing crystals and stones of unwanted energy. It's also a much quicker way to clear crystals than any of the above methods. To smudge them, pass you stone several times through the smoke of burning cedar, sage, sweetgrass, or incense. Commercial incenses with complex, perfumy smells may not clear as fully or as quickly as an herb like sage or a more basic incense like Nag Champa or Frankincense
Tap Water - COOL Tap Water: For a quick cleansing, you can also run your stones under cool tap water. Hot, very cold, or warm water is a no no because it can fracture some crystals and stones. Again, as with salt water, be sure that your crystals are not porous or soft, before putting them under the tap. Stone clusters and geodes are two types of stones that do not do well with water, as they may break apart and crumble. The stones mentioned as not doing well with salt water may also not do well with tap water.
Reiki-Seichim: Reiki-Seichim is another of my favorite methods of cleansing crystals. In a sense, it's channeling the universal life force energy to heal the crystal of negativity and unwanted energies. As a Reiki or Seichim practitioner, just treat the stone as you would any other being that needs healing, and set your intent to heal the stone of any negativity or unwanted energies.
Stone Clearing: Some stones will clear the negative or unwanted energies from other stones. I am familiar with doing this with quartz crystal clusters, amethyst clusters, and selenite. Place the stone to be cleared on a the "clearing" stone, and leave for 24-48 hours.
Flower Water: You can also clear crystals and stones in flower water. Soak the stone or crystal in water with the petals of rose, honey suckle, orange blossoms, jasmine or others for 24 hours. Again, the same cautions apply regarding stones that don't do well in water.
Ask: This is too simple for most peoples' need for ritual, but it does work wonderfully. Simply ask the Divine (God/Goddess/Universe or whatever your higher power is called) to clear and energetically cleanse your crystal for you. You can also simply ask the crystal to clear itself.
Whichever method you choose, the exact length of time needed for clearing varies according to personal taste and the state of the crystal. Trust your intuition and higher self to lead you to the best methods and lengths of time for you and the stone.