How To Start A Freshwater Aquarium – Guide & FAQs

Do you have a new freshwater aquarium to start and you don’t really know how? You have come to the right place. We have put together this complete guide to provide you all the information you require to safely cycle a freshwater tank and answered the most common FAQ on cycling a tank.

How To start A Freshwater Aquarium

Starting a new freshwater aquarium is fun and exciting. As soon as it’s filled with water we can’t wait to start adding fish.
But rushing a new tank start up is a sure road to disaster. Why?
Because the health and well being of an aquarium depends on billions of invisible microbes that keep the biologically balanced and safe for the fish.
That’s right! Most of the aquatic life in your freshwater aquarium is made up of microscopic bacteria.
These bacteria form the “biological filter”, which breaks down harmful fish waste.
Without these helpful microbes, your aquarium would be an ecological disaster.
In fact, most new aquarium problems are caused by adding too many fish before the beneficial bacteria have had a chance to settle in.
Want to know how to properly start a new aquarium and avoid common pitfalls? Here’s how.

Ammonia and aquarium fish

It’s important to understand a little biology when starting up an aquarium. Aquarium fish require protein in their diet. Ammonia (NH3) is a byproduct of protein metabolism and is excreted through the gill membranes.
A small amount of ammonia comes from the urine. Solid fish waste falls into the gravel where it decays and also releases ammonia.
Uneaten fish food (flakes and pellets) decompose, adding ammonia to the aquarium water. Ammonia is toxic to fish.
In nature, the ammonia is diluted by thousands of gallons of water. It’s also rapidly detoxified by bacteria and even adsorbed by plants and algae.

However, the aquarium is very different. It’s a closed environment. Your tank is not spring fed. There’s no stream flushing it with fresh water.
Home aquariums have a much higher ratio of fish per gallon than in the wild.
The fish population in an aquarium is thousands of times higher than in a natural stream or lake. This means ammonia can easily build up to harmful levels in the tank.
When ammonia levels rise, it prevents the fish from excreting ammonia from their bodies. This can cause the fish to suffer convulsions and even death if the ammonia level is very high.

Long term exposure to low levels of ammonia causes problems with the gills, liver, and kidneys.
Over time the fish will become weak and susceptible to disease problems. Their immune system won’t be able to fight off stress and diseases that normally wouldn’t affect them.
Fortunately, there’s a group of beneficial, non pathogenic bacteria that detoxify ammonia, keeping the aquarium water safe for the fish.

Understanding nitrifying bacteria

The bacteria we’re interested in are called nitrifying bacteria. That’s because they use the nitrogen as a “food” or energy source.
There are two types of nitrifying bacteria that work together to rid the aquarium of ammonia.

This two step detoxification process is called the nitrogen cycle.

  • The first type of bacteria are called ammonia oxidizing bacteria (AOB). This is a technical term for bacteria that use ammonia for energy, converting it to nitrite (NO2-) in the process. Nitrite is also toxic to fish, but we’ll talk about it later. Ammonia oxidizing bacteria go by names like Nitrosomonas and Nitrosospira. The conversion of ammonia to nitrite completes for first step.
  • Next, nitrite oxidizing bacteria (NOB) take over. Nitrobacter species convert nitrite into relatively harmless nitrate (NO3-).

The conversion of ammonia to nitrite, then to nitrate completes the nitrogen cycle. This what the phrase “cycling an aquarium” means.
The nitrifying bacteria have run through the nitrogen cycle and formed stable colonies in the aquarium.
These colonies form the “biological filter” and keep the water free of harmful ammonia and nitrite. Nitrifying bacteria can be found floating around in the aquarium water, but they tend to form colonies on surfaces like gravel, ornaments and even on live plants.
They’ll colonize just about any surface, even inside the aquarium filter.
Most aquarium filters provide some type of special biological filter media for the bacteria to attach to.
The truth is, nitrifiers growth throughout the aquarium, not just on bio filter media. If you’re thinking nitrifying bacteria are critical to the health of the tank, you’re 100% correct.
Here’s how they get into your aquarium.

Where do nitrifying bacteria come from?

There are many varieties of nitrifying bacteria in nature. Some types live in freshwater, some in saltwater and others live in both!
Nitrifiers can be found in garden soil, on pebbles in a stream, living ocean sediment and in sewage treatment plants. They’re almost everywhere, even in water vapor floating through the air.
In the early days of fish keeping, no one knew anything about nitrifying bacteria or biological filtration.
People added a layer of soil, pebbles and live plants when they started a new tank.
Nitrifying bacteria were carried into the aquarium on all these aquascaping materials and even on the live plants and fish. This helped “seed” the new aquarium with bacteria, starting-up the biological filter.
Keep in mind that no one knew about ammonia and nitrite toxicity. They didn’t even have aquarium test kits to check on the water quality.

freshwater aquarium

In reality they were either very lucky and happened to add the right bacteria by accident or they lost a lot of fish due to ammonia and nitrite build up.
Unfortunately, it’s much the same today. Most new aquarium hobbyists know nothing about nitrifying bacteria, ammonia or nitrite.
They simply add fish and start feeding them. If they’re lucky, the fish survive the ordeal of swimming in ammonia and nitrite.
But this is stressful and often leads to disease problems a month or two after setting up the tank. If the fish are over fed or too many fish are added at one time, the ammonia level soars, killing the fish.
This is called New Tank Syndrome. But starting a freshwater aquarium doesn’t have to be like this.

Preventing new tank syndrome

Today we know about biological filtration. We have ammonia and nitrite test kits to check on water quality. We even have bottles of nitrifying bacteria to help seed and start up a new aquarium.
We no longer have to hope the new aquarium will be OK. We’ve got the tools we need to start the tank off right. Right? Not exactly.
Even with the right tools, we still sometimes get it wrong. The aquarium trade came up with a name for it, called New Tank Syndrome.
The easiest way to explain it is by describing what happens in the invisible world of new aquariums.
Imagine a newly set up freshwater tank. It looks beautiful.

Crystal clear water, nicely aquascaped and home to a variety of tropical fish.
The problem is, the aquarium is biologically sterile. The fish are eating and producing waste but there aren’t enough nitrifying bacteria to detoxify the ammonia.

The ammonia is slowly rising. But It takes time for the nitrifiers to reproduce in the aquarium.
Nitrifying bacteria are really slow growers. They reproduce once every 24 hours. This is an unusually long time compared to other microbes.

It’s going to take four to six weeks for the bacteria to fully form a healthy biological filter.

Over this time period the ammonia and nitrite will rise and fall as the biological filter develops. Ammonia causes stress and tissue damage. Nitrite prevents the fish’s blood from absorbing oxygen. How you care for the aquarium over this break-in period determines success or failure.
But don’t worry! We’ll explain everything you need to know about cycling your new aquarium.

How to start the cycling process

There are several ways to start up and cycle a new tank.
For our example we’ll use a 10 gallon aquarium.
We’ll describe each method along with the pros and cons.
Each method will cycle the tank but requires following certain procedures to make it work.

1 - Add fish and hope for the best

The most common cycling method is to fill the aquarium with water, start the filter and stabilize the water temperature.
Then, add three fish to the tank. You can add more fish later, after the aquarium cycled.
Rushing only results in problems.
Feed the fish once a day and only what they’ll eat in a few minutes.
The more you feed, the more ammonia is released into the water.
Here’s the secret.

The nitrifying bacteria can’t reproduce unless there is something to “eat.”

They get their energy from ammonia. So, a new tank needs bacteria AND ammonia.

But not too much ammonia or it will harm the fish. That’s where many aquarists go wrong. They add too many fish or add too much food.
This causes ammonia to build up faster than the bacteria can consume it.

But remember, the nitrogen cycle is a two step process.
The first step converts the ammonia to nitrite (also harmful).
The second step converts nitrite to nitrate.

This is where test kits come into the picture. You’ll be able to track the rise and fall of the ammonia, followed by the rise and fall of nitrite, over the first four to six weeks after the fish.
When the ammonia and the nitrite levels fall to zero, the aquarium has cycled.
Once this occurs, you can add a few more fish to the tank. But don’t add all the fish. That’s because the biological filter only grows to match the waste load of the tank.
Every time you add more fish, the biological filter has to grow to match the new fish population. But it happens much more quickly after the initial cycle.
Just keep an eye on the ammonia and nitrite levels as you add more fish to the tank.

aquarium with fish
  • PROS

    - The “old fashioned” proven way to slowly cycle the aquarium
    - Prevents stressful conditions on new fish due to ammonia and nitrite

  • CONS

    - Depends on “luck” to introduce nitrifiers to the aquarium
    - Novice aquarists tend to rushing the process causing ammonia and nitrite spikes
    - Can take a long time if few bacteria are introduced
    - May require water changes to reduce ammonia or nitrite to protect the fish

2 - Seeding bacteria from another aquarium

Old time fish shop owners knew they could improve the cycling process by seeding a new customer’s new aquarium with bacteria from a shop tank.
This was done by adding a handful of seasoned aquarium gravel to the new tank.

An easier way is to put an old, dirty filter cartridge into the aquarium. Squeeze it out into the tank so bacteria laden “grunge” goes everywhere.

The idea is to add a living culture of nitrifiers and some fish at the same time.
Remember, just adding bacteria won’t help. You must add an ammonia source (fish) to stimulate the bacteria to reproduce and colonize the aquarium.

home fish tank
  • PROS

    - Works well if the filter cartridge is coated with nitrifiers
    - Adds a variety of beneficial bacteria including nitrifiers

  • CONS

    - The cartridge may also introduce algae to the aquarium
    - If the old aquarium contains sick fish, it could introduce pathogens

3 - Adding a bacteria starter

There is a lot of misinformation on the web about bacterial aquarium starters.
Some people say they’re all “snake oil.” Others say they work great.
Here’s what you need to know.
Some liquid bacteria products contain nitrifying bacteria. Some products contain non-nitrifying bacteria called heterotrophs.
Heterotrophic bacteria digest organic matter, like fish waste, uneaten fish food and dead algae.
The bacteria reduce ammonia by ingesting the nitrogen before it forms ammonia. These bacteria don’t nitrify, meaning they don’t convert ammonia into nitrate. This means that they won’t do a good job getting rid of the ammonia released by the fish.

An established aquarium has both types of bacteria working to rid the tank of organic sludge, and ammonia and nitrite.
Adding heterotrophs won’t hurt, but they don’t cycle the new aquarium.
You may have read that nitrifying bacteria won’t survive in a bottle because there isn’t enough oxygen. The truth is, nitrifiers are very resistant to low oxygen conditions, otherwise they wouldn’t survive in nature where they’re subjected to a variety of adverse conditions.

Research shows that a properly manufactured culture of nitrifying bacteria will survive for several years in a liquid formulation.
It’s important to read the product label or visit the manufacturer’s website to determine if the bottle contains true nitrifying bacteria.

goldfish in aquarium

There is also some confusion as to how these tank starter products work.
The better aquarium starters say to add the bacteria and fish at the same time. As we’ve discussed, the nitrifiers need the ammonia produced by the fish to activate and start to colonize the aquarium.
Pouring in the bacteria and waiting a week does nothing! The biological filter can’t activate unless there is an ammonia “food” source to feed on.

That’s why the product instructions say to add some fish to the aquarium right away. Understand that adding live nitrifiers does not eliminate the cycling process.
Instead of six weeks, you may see the tank cycle in two to four weeks. You’ll still see ammonia and nitrite levels rise and fall, but the levels will be much lower and less stressful to the fish.

  • PROS

    - No chance of adding algae or fish diseases
    - Ensures your adding live nitrifiers
    - Reduces the peak levels of ammonia and nitrite

  • CONS

    - Some products don’t contain real nitrifiers

4 - Fishless cycling

The idea of fishless cycling is simple.

Instead of using fish to create the ammonia necessary to energize the biological filter, just add ammonia.

This way of cycling an aquarium was made popular with saltwater hobbyists. Instead of subjecting sensitive and expensive marine fish to harmful ammonia and nitrite spikes, the aquarium would be “artificially” cycled without any livestock.
This makes sense for in freshwater aquariums too.
There are two ways of doing it.

  • Many aquarists simply add several pieces of flake food to the tank along with live nitrifiers. The food will degrade and add ammonia to the water. It’s difficult to know how much ammonia the food adds. Testing with an ammonia kit will allow you to track the initial rise in ammonia and the corresponding spike of nitrite. You must add enough food to get the ammonia up to about 0.5 ppm.
  • Another method is to add household ammonia to the tank. Opinions vary but the idea is to add ammonia to the water until it reaches 0.5 ppm. An easy way to figure out how much ammonia to add is to dose a one-gallon bucket of water. Test the water for ammonia after adding several drops of ammonia.
danio in fish tank
  • PROS

    - Eliminates fish stress during the cycling period
    - No need for frequent water testing to protect the fish during cycling
    - Forces the biological filter to grow larger all at one time
    - Lets you add lots of fish after the tank has cycled

  • CONS

    - Fish food boosts organics in the water.
    - Decaying food can cause a heterotrophic bacteria bloom.

Cycling a Freshwater Aquarium FAQs

discus in fish tank

My tank’s been running for a week and my test kits shows no ammonia. Is my tank cycled?

No. It is not unusual for testing to show no ammonia until the second week. Your aquarium is just beginning to cycle.

My ammonia level went up then dropped to zero. Is my tank ready for more fish?

Probably not! You must also test for nitrite. It is normal for the ammonia to drop to zero while nitrite is still high.

My new aquarium became cloudy after the first week. Is this ammonia?

No. Ammonia in the aquarium is colorless and odorless. The cloud is caused a bloom of heterotrophic bacteria. They’re feeding on uneaten fish food and other organics. Reduce feeding until the water clears.

My new tank became hazy. I emptied it, washed everything and started over. Now it’s hazy again.

Every time the tank is emptied and cleaned the break in process has to start over again. Reduce feeding a little if the water gets hazy. There should never be uneaten food in the aquarium or filter if cycling with fish. A slight haze is normal and will clear if left to balance out naturally.

Should I run a UV sterilizer during the cycling process?

No! Turn it off until the aquarium has cycled. The young aquarium hasn’t developed stable bacteria colonies yet. Once the tank has cycled and formed colonies on the gravel and other surfaces it’s OK to run the UV.

My pH is dropping. Is this normal?

The biological filtration process produces acids and use up alkalinity (KH). If the aquarium has low KH to begin with, the pH will tend to drop along with KH. Monitor both with test kits. Keep the pH above 6.8 during the cycling process. Add a little carbonate pH buffer if necessary, to stabilize the pH.

The cycle has stalled for several weeks with no ammonia and high nitrite. What can I do?

Check the KH level. When the KH level falls too low, the nitrite oxidizing bacteria may become inactive. Bring the KH level up to 5-6 dKH and the bacteria will activate and convert nitrite to nitrate.

I added a tank starter and a few fish. It’s been several weeks and my ammonia is still rising.

Check the product label or manufacturer’s website to find out if it contains nitrifying bacteria. If the product contains heterotrophic bacteria, you will have to add nitrifiers to kick-stark the cycle.

I’m cycling with fish. My nitrite level is high. Should I change water?

Cycling an aquarium with fish can be tricky if ammonia or nitrite levels reach harmful levels. Water changes will dilute the toxins but also “rob” the bacteria of food needed to form a larger biological filter. Don’t let the fish suffer. Make the water changes necessary to bring the levels down while reducing feeding until the tank cycles.

I used a dirty filter cartridge to start my new aquarium. The water looks dirty. Is this OK?

Yes. The slime and sludge we normally call “dirt” is teeming with all kinds of microscopic life. These include nitrifying bacteria and other helpful microbes. They tank will clear all on its own. Resist the urge to change water or siphon the gravel during this break-in phase.

Final thoughts on cycling a freshwater aquarium

We’ve discussed the importance of biological filtration and ways to cycle a new freshwater aquarium.
It’s not difficult to get through the break in period when you know how it works and what to expect.
Rushing the process never works because the nitrifying bacteria are unusually slow growers. There’s just no way to make them work faster! The key to success is to allow the cycling process to proceed at its normal pace.
It may seem like a long process but once the tank is cycled you can start adding fish and enjoy a healthy trouble-free tank for years to come!

How To Start A Freshwater Aquarium - Guide & FAQs