Of all the aspects that are part of successfully keeping fish, nothing matters more than cycling the aquarium -- often referred to as “breaking in the tank.” Unseen within every aquarium -- and aquatic ecosystem in the wild -- is a biological cycle that breaks down toxic wastes into less toxic ones. Without this essential process, fish could not live for long in the water that is their home.

The difference between natural aquatic habitats and aquariums is that fish in captivity live in much less space than they do in the wild, so the concentrations of toxic compounds rise far more rapidly, with vastly more serious consequences. A small fish in a 100-gallon tank has far less water than it does in its natural environment, but we certainly wouldn’t be happy keeping a single, small fish in a large aquarium, so we have to pay close attention to the biological cycling of the tank.

Basically, two sets of naturally occurring bacteria are responsible for the process. The first set converts ammonia -- which is very toxic to fish at very low concentrations -- by consuming the ammonia and changing it to nitrite. Nitrite is also quite toxic to fish even in tiny amounts, so the second set of bacteria convert this compound to nitrate (note the “a”). Nitrate is not considered harmful to freshwater fish, but it can be used by plants and also by algae. The best way to reduce nitrate levels is by doing partial water changes on a regular basis, which dilutes the concentration of nitrate in tank water.

The thing to keep in mind is that the more ammonia and nitrite there is, the greater the number of bacteria there must be to efficiently and effectively convert these compounds. Many fish will become sick when exposed to relatively small amounts of either one because their immune systems do not function well under the physical stress of this toxicity. In fact, this is typically why fish in new aquariums “mysteriously” become ill and then die. The first seven or eight weeks are critical to the health of the fish in a new setup because there aren’t enough bacteria in the tank.

The bacteria multiply during these initial weeks and colonize all surfaces in the aquarium. During the first couple of weeks, ammonia is usually quite high if there are a lot of fish in a new tank, but as the number of bacteria increase, ammonia levels begin to drop and finally become unmeasurable when using a test kit. As ammonia goes down, nitrite levels begin going up because there aren’t yet sufficient numbers of the second group of bacteria. Tank water can therefore still be toxic for another five to six weeks -- on average -- before nitrite becomes unmeasurable.

There are two things you can do to help the fish during this break-in period. First, don’t add all the fish at once to a new aquarium. It’s better to add a few and let the tank cycle completely before adding the rest. By that time there’s usually enough bacteria that the additional fish are not as much of a problem.

Second, make sure you have a filter that includes a place for bacteria to colonize. Filters typically have materials in them that have lots of surface area over which water can flow, which increases the total population of bacteria in the aquarium system. The other location that has lots of bacteria is the gravel, because the total surface area of all the grains is also quite large.

The average cycle time for most aquariums is about 5 weeks.

Fishless Cycling As an alternative to cycling your tank with fish you can just throw a piece of raw shrimp in your tank. It will decay and produce an ammonia spike and begin the nitrogen cycle the same as fish poop.

In order to protect these bacteria, you don’t want to replace the filter material or clean the gravel too well. Simply rinse the filter material in a bucket of tank water when doing a water change. If you clean the gravel, do only one-third to one-half each time you do a water change. This will ensure there’s always sufficient bacteria to keep the water healthy for the fish.

You might be wondering if the water changes wouldn’t do the same thing as biological filtration. If there were only a few small fish in a moderately large aquarium, and you changed most or all of the water at least once a week, you might be able to eliminate the need for additional biological filtration, but because most aquariums are stocked with a lot of fish, water changes simply can’t keep up with increasing ammonia and nitrite during those first weeks.

Once your aquarium has cycled, the fish will have good water quality to thrive in. By not overstocking the tank or overfeeding the fish, you can make sure the water quality is always good for them.

Bob Roberts has been keeping fish more years than he cares to remember, and has written extensively on the topic of aquariums.