There are different ways to cleanse a stone, the easiest is to smudge it with sage. Light a stick of sage or a sage cone and blow it out so it smoulders. Hold your crystal in the smoke and let it rise around all sides of the crystal. Do this until you feel it has been cleansed enough. It’s great to sage yourself too as it will cleanse your own energy. Advantages quick and easy with no discolouring or damaging of your stone Disadvantages you may smell of smoke
Another way is to soak in salt water by mixing a ratio of 3 tsp of salt to half a gallon of water. Place your stones in the mixture and soak for 12 hours. Disadvantages time consuming and some stones may dissolve in water
Rain water is another choice as it will wash away any negativity in your stones. Use your own intuition on how long to leave them out depending on how much it rains.
Burying your stones in the earth for 12 hours can also cleans and rejuvenate them, just remember where you bury them!
Cleansing by sunlight or moonlight is a definite favourite. Moonlight is a stronger but not always available and some stones may fade if left for too long. This also charges your stone
Another way to charge your stone is to place on an amethyst or Citrine cluster or piece of selenite as they naturally replenish their energies