As mentioned in our blog post on What is the Nitrogen Cycle? ammonia is a toxic waste that is excreted by fish or caused by decomposing plant matter and uneaten fish food. At low levels, ammonia is stressful for most fish and other inhabitants -- at higher levels, it is deadly. Fortunately, naturally occurring bacteria are present in most established systems that converts this ammonia to nitrite and in turn, to the less toxic nitrate.