Ammonia is processed in nature (in ponds, lakes, and rivers) through tons of aerobic bacteria that transform Ammonia into Nitrites. These bacteria (Nitrosomonas) feed on the energy released by the reaction (chemical reaction).
Nitrites are also quite harmful to fish. Fortunately, another group of also aerobic bacteria called Nitrobacter oxidizes nitrites into nitrates.
Again, these bacteria feed on the energy released by the reaction.
Finally, the nitrates formed by this process are less harmful than Ammonia or Nitrites. Plants and Algae consume Nitrates, keeping their levels low.