*minor spoilers*
-Once you get to the snow area, you'll get quite a few.
-As you obtain more Star/Blood stones and open up more rooms at the End of Time, there will be 4 merchants who will always have in stock 1 of the essences- one will have fire, one will have water, etc. They restock these every time you level up.
-Any merchant, particularly crafting-material selling ones (buy at first opportunity!).