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Definition: Ammonia is a toxic substance that builds up in the aquarium, particularly in a newly setup tank. Ammonia is the first step in the nitrogen cycle, and is produced as a byproduct of protein breakdown such as, uneaten fish food and fish excreta. It is removed by beneficial bacterial that are able to convert it into nitrite. NH3 occurs only in alkaline water, appearing instead as ammonium (NH4) when the water is acidic.