Whether or not you take the energetic claims about crystals literally, there's a practical reason to cleanse them regularly: they pick up dust, oils from your hands, and — more importantly for a spiritual practice — they become associated with whatever you were feeling the last several times you held them. A stone you leaned on hard through a rough week can start to feel "heavy" simply because you've loaded it with that association. Cleansing is a reset, for the stone and for you.
Moonlight: The gentlest and most widely used method. Leave your stones on a windowsill or outside overnight during a full moon, or any clear night. Moonlight is considered safe for essentially every crystal, including more delicate or color-sensitive stones that direct sunlight could fade.
Sound: A singing bowl, bell, or even a clear, sustained clap held near the stone can shake loose stagnant energy. This is a good option when you want something quick and don't have access to moonlight or running water.
Smoke: Passing a stone through the smoke of sage, palo santo, or incense is one of the oldest cleansing methods, and it works well for stones that shouldn't get wet. Hold the stone in the smoke for a slow count of ten, setting an intention as you do.
Earth: Burying a stone in soil for 24 hours lets it return briefly to where it came from. This works especially well for grounding stones like Black Tourmaline or Smoky Quartz, though it's worth marking the spot so you don't lose track of it.
A caution on water: Running water is a classic cleansing method, but it's not safe for every stone — Selenite dissolves, and many stones with iron content can rust or discolor. When in doubt, choose moonlight, sound, or smoke instead.
However you cleanse, take a moment afterward to set an intention for the stone's next chapter of use — what you want it to support, or what you want to feel when you hold it. The cleansing clears the slate; the intention gives it direction again.