Water is a hazard in the Phoenotopia games. It poses a threat to Gale because she doesn't know how to swim. Additionally, certain enemies like Toads and Fish can also reside in the water. In earlier parts of the game, water appears sporadically in some areas, mainly in Duri Forest and the underground caves beneath Atai City. Later, though, it becomes a much more prominent hazard, especially in Misty Gorge/Moonlit Ravine, Mul Cavern, and some parts of Daea.

In Phoenotopia, water has the same effect as bottomless pits; if Gale falls into it, she'll respawn on the nearest platform and take some damage. This can be remedied by buying the Floaty Donut in Misty Gorge, which allows Gale to swim across the surface of water.

In Phoenotopia Awakening, Gale doesn't respawn right away if she falls into water; she will first go through a drowning animation for a few seconds before respawning. Water-dwelling enemies can now swim under the water too. Gale can also go underwater after buying the Floaty Donut, this time located in Moonlit Ravine; additionally, the Floaty Donut also allows her to dive underwater for a few seconds by jumping into it from a high ledge. Game fish can also be found in water, which Gale can catch using the Fishing Rod.