Most cave formations are created when rain water picks up carbonic acid from decaying leaves and eats away at limestone. The water picks up dissolved calcite as it flows through rock. When the water is exposed to air, carbon dioxide evaporates out of it and leaves calcite behind. This is the basic process that creates most cave formations. Cave pearls are formed when calcite is deposited in thin layers around grains of sand. Dripping water keeps them moving and keeps them from sticking to each other, at least until they get too big.
Source: http://weirdkatharine.tumblr.com/post/649665308709339137/my-favorite-things-27-cave-pearls