Rainwater seeping though the porous limestone quickly enters the aquifers contained in the network of cavities below. The cavities were formed during the last Ice Age when fluctuations in sea level periodically exposed more land.  Thousands of years of rain fall on the soft limestone so close to the surface caused their roofs to collapse. After the sea level rose ponds formed at the surface. 
Snorkeling and diving cenotes is a new frontier. It evolved in the mid-1980s when professional explorers began to descend into the many "natural wells" of the Yucatan peninsula. Many underwater caves were discovered and surveyed. To date, it is estimated that more than 200 miles of underwater passageways have been explored. This involves hundreds of cenotes linking to more than 50 cave systems, and the list grows each year.