Well, it would be suggested that you don't put the crystals directly in the water if you have the intent of having the elixir consumed or otherwise placed internally into you. This is because there are a number of stones (even the common ones) that are poisonous when consumed, or will break off in water (crystal formations such as amethyst and quartz). Trust me, you don't want to be drinking crystal dust and pieces chipped off. Generally tumbled stones are safe, but it's always good to take the procaution.
Basically, you could start with two containers. The largest will hold the water supply. The smallest, which will go inside the first container, will have your crystals (No water contact whatsoever) The energy from the crystals vibrates throught the thin material, and into the water, which produces the same effect if you had the stones in directly. As said before, it is always nice to consider the hour/day you make the elixir, along with the option of setting it in the sun or under one of the moon phases. How long your elixir is charging under an element/stone mix is completely up to you or the recipe you follow.