The water is clear due to the absence of plankton and suspended particles. Plankton is the base of the food web in all oceans and, because there is little plankton in the tropics, tropical ocean water is nearly sterile in comparison with the fertile waters of the temperate oceans.

The crystal clarity of Caribbean waters is the result of low nutrient levels and minimal sediment. Unlike northern coastal waters, which are rich in plankton and algae (giving them a murky or green appearance), much of the Caribbean is "oligotrophic," meaning it is relatively desert-like in terms of microscopic plant life. This lack of organic matter allows light to penetrate deeper without being scattered. Additionally, many Caribbean islands are small and lack large river systems; without massive rivers dumping silt and mud into the sea, the water remains pristine. This clarity is further enhanced by the white calcium carbonate sand—made from crushed coral and shells—which reflects sunlight back up through the shallow water, creating the vibrant turquoise and teal hues that make the region a world-famous destination for snorkeling and diving.