As the Little Falls Dolostone was slowly buried by new sediments, the temperature slowly rose from perhaps 20 degrees C to 175 degrees C or slightly higher. This burial took about a 200 million years and reached a maximum depth of approximately 5 kilometers about 300 million years ago. As the temperature rose, molecules from the organic material that had been holding in solution the quartz dissolved from sand were broken apart so that the quartz could form crystals. Because burial was extremely slow, formation of the quartz crystals was also extremely slow allowing many to grow clear and gemmy which is why they are called Herkimer Diamonds or Little Falls Diamonds.
The other minerals formed before, during and after the slow crystallization of the quartz. Dolomite and pyrite often formed earlier while calcite sometimes formed at the same time as the quartz, but more often calcite sometimes formed at the same time as the quartz, but more often afterwards. The hydrocarbon black spots in the quartz crystals, the black tar-like material in the cavities, and the microscopic grains that make some of the quartz crystals brown or black are all remnants of the fossil organic material that was essential to the formation of the unusually clear and flawless crystals.