Jellyfish Lake is connected to the ocean through fissures and tunnels in the limestone of an ancient Miocene reef.

The golden jellyfish, Mastigias papua etpisoni, and possibly other species in the lake, have evolved to be substantially different from their close relatives living in the nearby lagoons.

[1] The stratification of the lake is caused by conditions which prevent or restrict the mixing of water vertically.

All organisms that require oxygen live in this layer including the jellyfish, a few species of fish and copepods.

Biologist William Hamner estimated that about 2.5% of the lake's volume is exchanged during a tidal flow.

[2] Research has shown that the jellyfish population plays an important role in mixing the water and its content of oxygen and nutrients in the lake.

The top three meters of this layer contains a dense population of bacteria, at least one species of which is a purple photosynthetic sulfur bacterium.

He also proposed that the jellyfish living in four other Palauan marine lakes were distinctive enough to deserve recognition as unique subspecies.

[11] However, since the release of that report in 1981, genetic testing has been done on specimens of Aurelia collected from locations throughout the world.

Despite the close proximity of Palau's moon jellyfish cryptic species, Dawson and Jacobs stated that the molecular data suggested that they had not interbred for millions of years.

in other Palauan marine lakes and coves which all migrate west to east in the morning.

[8] Based on their extensive investigation of the disappearance of the golden jellyfish medusae, Dawson et al. determined that the most likely cause was an El Niño weather event that raised the water temperature, with the result that the symbiotic algae (Zooxanthellae) that live within the golden jellyfish medusae and the syphistomae (scyphozoan polyps) could not survive.

[15] Dawson et al. also surveyed the golden jellyfish populations in three other Palauan marine lakes.

This was previously attributed to turbulence generated by scuba diving that caused disturbance of the toxic layer.

[8] The moon jellyfish exhibited unusual damage in the 1998 time frame; however, the population seemed no smaller than usual.

[20] Although both species of jellyfish living in the lake have stinging cells (nematocytes), they are not in general powerful enough to cause harm to humans.

Saltwater crocodiles are native to Palau but there has only been one death attributed to them in recent times and they are generally not considered a threat to divers.

In 1977, the maximum safe threshold level for H2S was set at 10 ppm,[22] and concentrations at the bottom of the anoxic layer exceed that by eightfold.

However, the hydrogen sulfide concentration down to the chemocline at about 15 metres (49 ft) is reported to be zero, and if the anoxic layer is avoided, the H2S in the lake does not pose a risk for snorkelers.