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Aquasagnia split from its ancestor after spores carried from coastal waters into river deltas by the tides began germinating. This isolated population adapted to the freshwater environments of western Darwin. Cell walls are thicker and dormancy can last longer due to having a more hardy spore state in which the cell desiccates significantly. The lack of water in the cell, along with specialized proteins, slow down cellular processes and degradation. They can be carried further by wind and bloom more readily when conditions are favorable. Like its ancestor, this species can form dense clouds near the surface and cells shrink into spores when conditions are dry or saline.

Aquasagnia is common throughout subtropical and temperate western Darwin, especially in slow-moving and stagnant water. Dense blooms occur when nutrients spike, often making bodies of water temporarily anoxic. Even temporary bodies of water formed during floods may have blooms due to the opportunistic nature and abundance of spores.