An aquarium's nitrogen cycle is the process a new aquarium undergoes to establish bacterial colonies, according to About.com. As fish excrete waste and plants inside the aquarium decay, bacteria grow to convert this waste to less toxic byproducts. The fish are at risk until there is enough bacteria.
In the initial state of the nitrogen cycle, the waste products of fish are broken down to ammonia, which can be toxic if left for three days or more. In the next stage, bacteria oxidize and eliminate the ammonia but produce nitrite as a byproduct, which is also toxic to fish. In the final state, different bacteria convert the nitrites to nitrates, which are not toxic in low levels. Changing the water routinely helps to control nitrate levels.