There are 9 Goddess Jewels to collect in the game. They can all be found in the Spring Mine on floors 60, 102, 123, 152, 155, 171, 190, 202, and 222. These are the only locations of the jewels in the game, and they will randomly generate into rocks that you must smash with your hammer. Each jewel can only be found once on the selected floor.
Tip: The easiest way to get the Goddess Jewels to appear is to save before entering the floor with a Goddess Jewel. Go down to the room using the stairs and start to hit rocks. If you are having troubles finding the jewel and are using a lot of stamina, revert back to your old save. That way, you save yourself the energy, and the floor will be reloaded when you load up your save.
Unfortunately, it is randomized. Even when saving and reloading on the same floor, the Goddess Jewel will appear in a different rock then it will before you reloaded. Just keep trying, and you will eventually find the jewel.