The rock islands were created over 35 million years ago as a result of the collision between two tectonic plates. The massive Pacific plate subsided causing the uplift of the Philippine plate, thus exposing millions of years of oceanic deposition. Since its uplift, this exposed sea bed has been carved away by a variety of erosive forces. As rain water mixed with decaying vegetation a weak acid called humic acid was created which slowly began to eat away at the limestone rock island . This erosive force was particularly damaging in pockets where the vegetation accumulated in mass. The result was that steep sided pockets were carved out of the limestone.

These pockets continued to carve deeper and deeper into the limestone until the salt water lens was reached at sea level. At the time that these pockets were formed, the world's sea level was as great as 300 feet below modern day sea level. Through geologic time the polar ice caps, holding huge reserves of sea water, began to melt. The world's oceans began to rise and thus sea water began percolating through the porous limestone to create true salt water lakes.

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