Xel-Ha is a unique location in all facets of underwater exploration.

Only the fjords bordering the Arctic Ocean share the specific characteristics caused by the simultaneous phenomena of halocline and thermocline, witnessed in Xel-Ha. Warm, dense, salty water from the sea, which cannot immediately combine with cool freshwater of lesser density, produces this visual effect reminiscent of a mirage. Whilst swimming, a separate layer of liquid can be seen on the surface, like water on oil, but this is in fact freshwater floating above seawater of greater density.

Xel-Ha houses over 70 recorded species of freshwater and seawater fish, including yellowtails, parrotfish, surgeonfish, jackfish, sergeant majors, grunts, snappers, bonefish, stingrays, chubs, doctorfish, and an occasional barracuda. The endangered queen conch inhabits Xel-Ha under careful monitoring and protection. Temporary visitors to the inlet include sea turtles and manatees.