This is not an official term.
The waters in the Pit and the swamp of Karda Nui contained a mutagenic substance created by a reaction between energies leaking out of Karda Nui and the ocean water of Aqua Magna. This mutagen caused those exposed to it to permanently mutate to resemble sea creatures, including making them able to breathe water and unable to breathe air.
Notes
Identity
The mutagenic agent wasn't sentient.1
Pit mutagen wasn't sentient or alive in any way.2
The mutagenic agent was a substance in the water.3
Pit mutagen was not related to the substance that transformed the Bohrok-Kal.4
Pit mutagen was not always present in the water.5, 6
Pit mutagen wasn't natural, nor was it intentionally placed.7
Pit mutagen wasn't released intentionally.8
Where the mutagen originated from was tied into where Voya Nui originated from.9
The mutagen wasn't more concentrated or potent before being released into the water.10
Pit mutagen wasn't made by anyone or anything known by story year 2007.11 It also wasn't released by anyone or anything known.12
Effects
The speed at which beings were mutated depended on how much of the agent they were exposed to.13
Potency of mutagen was less relevant than length and extent of exposure to it.14
The mutagenic agent took effect pretty quickly.15
Some aspects of the mutations caused by the Pit mutagen occurred very quickly, and others did not.16, 17
Some aspects of mutagen happened right away, others took longer. The Barraki continued to mutate over the thousand years they were exposed to it.18
The change to water breathing happened very quickly, otherwise beings would drown. The Pit was far enough beneath the ocean that beings couldn't swim to the surface fast enough to avoid the mutagen.19
If a Matoran's air bubble ran out, they'd probably drown before mutating.20
Pit mutagen gave beings the ability to breathe water pretty quickly, within a few minutes.21
It wouldn't take that long for a being exposed to Pit mutagen to become a water breather.22
The mutagen removed the Barraki and the Toa's ability to breathe air, but that didn't mean it stopped previously amphibious beings from being able to breathe air.23
Beings couldn't be mutated to the point where they'd regain the ability to breathe air.24
Scuba gear would keep a being from breathing the water in, but it would not protect one's entire physical body from exposure to mutagen. The only known things that protected beings from exposure were the air bubbles used by the Matoran of Mahri Nui and vehicles like submarines.25
A being with a breathing apparatus would still be affected by mutagen unless the device also protected them from exposure to the water.26
A being with a Kaukau would still mutate and grow gills because their physical body would be exposed to the water.27
It would take between hours and a day or two for a Matoran from Mahri Nui to develop the characteristics of sea creatures.28
It'd make sense for all mutated inhabitants of the Pit to be based off sea creatures because having those traits would make it easier to survive under the sea.29
Pit mutations weren't limited to just one sea creature.30
If a being in water with Pit mutagen swallowed some of the water, it probably wouldn't make much difference.31
It's possible the mutagen's effects were much more subtle on fully organic beings than they were on biomechanical ones, or it may have been that they took much, much longer to manifest.32
Pit mutagen seemed to affect purely organic creatures more slowly.33
Mutagen seemed to affect all members of a species the same way, much like Visorak venom did.34
If Zaktan were only partially exposed to mutagen, only the protodites exposed would mutate. He would mutate like the other Piraka mutated, not how protodites would have mutated.35
Inorganic beings like Maxilos would arguably be affected by Pit mutagen because inorganic objects, such as armor, are affected.36
Mutation was a physical change, it didn't affect things like morality.37
Pit mutagen worked much more slowly on Brutaka's species, among other creatures.38
Immunity
Brutaka's species had some natural resistance to mutation.39
The mutagenic agent affected almost everybody, but there was at least one known case of immunity.40
The Toa Inika weren't immune to Pit mutagen.41
The Toa Mahri were basically immune to mutagen.42
Nocturn was immune to Pit mutagen.43
Mata Nui would probably not be affected by Pit mutagen.44
Makuta could be affected by Pit mutagen.45
Brotherhood of Makuta armor wasn't resistent to Pit mutagen.46
Pit mutagen didn't seem to affect pure machines.47
The only thing able to reverse the Pit Mutagen was the Ignika, and possibly Mata Nui.48
Krahka wouldn't be immune to Pit mutagen.49
Zyglak were seemingly immune to Pit mutagen.50