The mutagen present in the Pit's waters was a type of energy that leaked into the water and mutated almost any being exposed to it. The mutation only took minutes of exposure to take its effect, and it was impossible to reverse without the Kanohi Ignika.
The substance was originally created as a type of power source, used to power the dome islands in the Matoran Universe (Metru Nui, Karda Nui, etc.). The mutagen was contained in two 'reactors' - one in Karda Nui and one on Metru Nui, which powered the lightstones around these domes. During the Great Cataclysm, power lines carrying the energy (one of them just beneath the Pit) cracked, releasing Mutagen into the ocean of Aqua Magna.
- The Barraki
- The Matoran of Mahri Nui - Reversed damage done to them by Karzahni
- Brutaka - Breathing Apparatus
- Spinax - Slightly
- The Piraka
- Most of the Pit's prisoners
- Makuta Bitil, Gorast and Krika
- Brutaka - Slightly
- The Zyglak species
- The Hydruka Rahi
- Organic Rahi
- The Toa Inika/Toa Mahri
- The mutagen affected the Kanohi Ignika, slowly dissolving it. As it did so, the mask let off small amounts of its power.
- On the way to the Chamber of Life, there was a large pool of water that the Piraka fell in that contained the mutagen.
- Botar was not changed by the mutagenic waters because he never stayed long enough to be affected (he deposits his prisoners and leaves within a fraction of a second before he can even get wet) - in fact, he never even noticed the Pit was flooded.
- The Toa Mahri were not changed into water-breathers by the Mutagen, but instead altered by the flash of energy the Ignika emitted as a cry for help.