Use the Mohs hardness scale. If you want a quick and general rule for water-safe crystals, then the Mohs hardness scale is your friend. Stick with crystals that are a 6 or higher and you should be fine. These are broadly considered water-safe.
Avoid iron ores or crystals that contain copper. A mineral such as Pyrite can rust when it comes into contact with water. Water could even cause some crystals to dissolve. An iron ore crystal should never get wet, especially not for a prolonged period of time, or by being completely submerged.
Crystals ending in “ite” are generally water-safe crystals. This might be another generalization but it’s right more often than not. The actual reason crystals end in the suffix, “ite,” is because there’s a push to standardize mineral names officially. It just so happens that the crystals that retain this name tend to be water-safe crystals. Stones like Malachite, Calcite, Hematite, Fluorite and Selenite should avoid water. They have a low water tolerance and are usually softer on the Mohs hardness scale too. This makes them easy targets to sustain irreversible damage.