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Aquatic systems are rich in microbes, including bacteria, archaea, protozoa, fungi, and microalgae such as diatoms. This microbiota is found within the water column and attached to all surfaces. On wet surfaces, this microbiota creates a sheltered scaffold known as the biofilm.

The bacteria can be autotrophic or heterotrophic. Autotrophic bacteria synthetize energy through photosynthesis or chemosynthesis using carbon from an inorganic source, such as carbonate. Heterotrophic bacteria get their energy from other organisms and therefore play important roles in both biodegradation and pathology. Both types have species that are anaerobic, aerobic, and facultatively anaerobic (preferring oxygen, but able to derive energy from other sources, like nitrate, when oxygen is in short supply).

The microbiota has a profound impact on animal health and water quality and should be considered part of the life support system.