Cycling Your Aquarium

Now that you’ve picked out your equipment and have your aquarium set up, you are ready to get started!  But first you have to learn a little about some basic water chemistry before you go crazy adding fish.

The Nitrogen Cycle

This image above is a basic chart of how the nitrogen cycle works.  Basically as various waste products decay, it first produces Ammonia.  Ammonia itself is harmful to your livestock, it will burn the gills of your fish and cut off their oxygen supply.

Fortunately in an established aquarium, the Ammonia get’s processed quickly into nitrite, which then will get processed into nitrate which is far less harmful to fish.  However, many invertebrate animals do not tolerate nitrates well.

For the most part, nitrates will be the end of the cycle in an aquarium setting, and it is less harmful to the fish, but first you must make sure that your nitrogen cycle is in full swing.

A brand new aquarium will not have any of the healthy bacteria needed to break down the waste materials in the beginning.  This becomes established over time.  The effect is that there will normally be a spike in ammonia when you first add livestock.  This is why it is very common to add only a very small (usually one) living creature (hermit crab, fish, etc…) in your tank to start off the nitrogen cycle.  Some people will even stick a piece of raw food in their tank and let it decompose.

Over time, the bacteria will grow that will consume the ammonia and produce nitrite, then quickly nitrates.  When the ammonia levels in the tank becomes undetectable, you know your tank has completed it’s cycle.

Most people new to the hobby probably don’t have test kits.  That’s fine at this point, just give the tank some time and it will stabilize.  If you wait about 3-4 weeks, you should be fine to start adding other livestock.

Controlling Your Nitrates

This is really the part of reefkeeping that tends to require the most maintenance.  Corals are the animals that are the most sensitive to Nitrates, so in a reef tank (a tank that has fish, corals, and other inverts) you will want to plan accordingly for nitrate control.

Nitrates are consumed in the aquarium by a couple of things:  denitrifying bacteria and macroalgaes.  But the process of consuming the nitrates is often too slow to be effective in an aquarium.  So most people will do water changes on a regular basis to control the nitrates.

Denitrifying Bacteria

Denitrifying bacteria is anaerobic.  That means that they grow in low oxygen zones in your aquarium.  The problem is that a reef aquarium requires good water flow which oxygenates the water.  This is why it is highly recommended to place lots of live rock in a reef aquarium.  The rock itself is simply structure that provides lots of caves and hollowed out areas where anaerobic bacteria can grow.  That’s what makes it live.

There is also strong arguments for deep sand beds, where anaerobic bacteria can grow in the sand.

The issue with these low flow anaerobic areas is that they will trap wastes over time which can build up until it gets released into the water stream causing a tank crash.

So, part of good maintenance is ensuring that you have a good clean up crew to control the waste build up and cleaning off the rocks every once in a while by blowing off those areas with a small powerhead or turkey baster.

Controlling Nitrates with Plants

I firmly believe in natural nitrate control with macroalgaes.  In the last few years, this has been a slowly growing movement.

Using a refugium area to keep macroalgaes such as Chaetomorpha (Chaeto for short) has been a long popular method of nitrate control.  A refugium is simply an area, such as a separate tank where the water cycles, where you can keep things such as macroalgaes, that are beneficial to the ecosystem of the aquarium, but you don’t want in your display tank.

Many people will grow Chaeto in a refugium because it is relatively fast growing, so it processes nitrates quickly and it does not release any chemicals into the water as some other plants will.

These plants do require light, which is why you will see strong grow lights over filtration areas.  I personally use a canister reactor filled with chaeto that I wrap with string LED grow lights.  I will discuss my DIY chaeto reactor in a future post.

One growing trend that I’ve tried that works well is using what is called an algae turf scrubber.  This is often a screen that is plumbed into the aquarium that the water flows down which is lighted by grow lights.  The screen over time will grow hair algae.  Hair algae grows very fast and uses up nitrates quickly.

I find with a good macroalgae system consuming the nitrates, you can keep nitrates down to an almost undetectable level.  In my case, I am able to keep even difficult corals alive and growing with very minimal water changes, by simply using my Chaeto reactor to process the nitrates in conjunction with a protein skimmer to remove waste products.


Basically, you want to start your stocking slowly, to allow your tank to cycle.  I will usually start with a small cleanup crew such as a few hermit crabs and snails.  After a few weeks, you can begin adding fish.  The last thing to work up to will be corals.  That will take time and an established filtration system.  But with a little patience, you can have a thriving reef in your living room.

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