How to clean aquarium after disease

How to Clean the Aquarium After a Disease Breakout

Experiencing a disease outbreak in your aquarium can range from a mild annoyance to a devastating loss. The big question many aquarists ask after a disease outbreak is “Do I have to clean out my tank?”


The thinking is the "disease causing" organisms are still thriving in the aquarium.
Aquarium hobbyists fear that adding new fish will just start the disease problem all over again.
So, they contemplate breaking the aquarium down and disinfecting everything. Some novice aquarists have thrown away their aquarium filter and gravel, thinking these items will forever contain fish diseases.

The truth is, you don’t have to replace your gravel or buy a new filter.
That’s the good news.
But it is possible to restart the disease cycle all over again if your unaware of proper fish health management.

Before discussing what to do after a disease outbreak, we’ll need to examine why tropical fish get sick in the first place.

Why tropical fish get sick

Aquarium fish don’t get sick without a reason. For a disease outbreak to occur, there must be three factors.
Without all three, disease problems rarely occur in the tropical fish aquarium.

  • The Host: The host is one or more of your fish
  • The Pathogen: Pathogens are parasites, bacteria, fungus or a virus
  • The Stress factor: Ammonia, nitrite, organics, extreme pH, water temperature, physical damage and over-crowding

The Host is easy. If you’ve got a fish in your tank, you have a potential host. The host is what the disease organisms attack and feed on.
“Pathogens” get a little more complicated. Many bacteria that cause infections usually live peaceful lives in your aquarium. When their population is small, and the fish are healthy, the bacteria don’t cause any problems.
But when fish get weak, wounded or stressed, the bacteria can attack the fish’s skin and internal organs. It’s similar with fungus. In a clean, healthy aquarium, fungal organisms like Saprolegnia, are not a problem.


But they can infest fish under the right conditions. Most parasites must have a fish host to keep their lifecycle going. Without a host to feed on, many parasites will die off. The truth is there is often a very low level of parasites in all aquariums. Healthy fish can fight off parasites under normal circumstances. Viral diseases are also not an issue when water quality is good, and fish are not stressed. The big take-away is stress is the number-one cause of fish disease problems in tropical fish aquariums. Here’s why.

How stress affects tropical fish

Stress is a generic term. We all know about stressful jobs, people who give us stress and other issues that can wear us down.
We’ll get sick if we’re under constant stress. That’s because stress inhibits our immune system.
Once our immune system is weakened, we’re vulnerable to all the colds and flu bugs floating around.

It’s the same with aquarium fish.

Exposure to ammonia, nitrite and even nitrate can wear down the fish’s immune system.
Aquarium water temperature that’s too cold, too warm or bouncing around will weaken the fish.
A dirty aquarium with a neglected filter or mucked-up gravel is a breeding ground for many disease-causing organisms.
Packing too many tropical fish into your tank will also increase the likelihood of disease problems.
It wears the fish down and pushes the waste-handling ability of the aquarium to the limit!
The combination of disease organism and stress is the knock-out punch that results in fish contracting disease symptoms.

Why fish recover from diseases

Tropical fish disease treatments are a complex subject.
We’ll keep it simple for this discussion. Many medications, like anti-bacterial treatments, simply inhibit the disease-causing organism just enough to allow the fish’s immune system a chance to recover and naturally mount a defense.
Anti-parasite treatments, like copper and formaldehyde, are poisons. At the right dose these chemicals kill the parasites but not the fish.
The idea is to knock back the parasites, so the fish can heal and develop an immune response. But remember the stress factor!


If your fish are swimming in a dirty, toxic aquarium, it’s going to be very difficult for them to get well. They may even all die despite using the proper medication.
If you don’t correct the water quality, the next group of fish will eventually get sick too. Medications only work if the aquarium water is safe for the fish.
But with aquarium test kits it’s easy to monitor and maintain a healthy aquarium. The chances are high that your fish will recover. But what do you do after the treatment is complete and the fish are looking ok?
Here’s the steps to take after you’ve finished a regimen of disease treatments in your aquarium.

Make a water change

For the typical freshwater aquarium, a water change requires nothing more than treating the new water with a dechlorinator and making sure the temperature is with a few degrees of the tank’s temperature.
Use a thermometer to be sure! Using a 10 gallon aquarium as an example, siphon out 3-5 gallons of water and replace with dechlorinated water.
If the gravel is dirty, use a gravel siphon to suck out the sludge. Small water changes are easy but after a disease problem and medicating, a large water change is recommended.
It will significantly dilute residual medications and flush out disease organisms. If your tank is really dirty or has detectable ammonia or nitrite, it may require several large water changes made over a couple of days.

Change the aquarium filter

While making the first water change, rinse out your aquarium filter.
A hang-on-back power filter is easy to remove and take to the sink.
Canister filters should also be emptied and thoroughly cleaned. Throw away old filter media and foam cartridges. You can wash the filter housing with soap and water. Just be sure to give it a good rinse.
There’s an old myth that traces of soap coat the filter and will poison the fish. The truth is soaps readily wash away under the faucet. Use new activated carbon in the filter. The adsorbent carbon granules will remove residual medications from the water.
Some tropical fish treatments will color the water. You may have to change out the activated carbon every couple of days until the water clears up.
Biological filter media can be rinsed with aquarium or dechlorinated tap water to remove sludge. Most of the beneficial bacteria live in the water and on the surface of the gravel. Rinsing bio-filter media won’t kill disrupt the biological balance of the aquarium.

Test the water

There is no way to know the condition of your aquarium’s water without testing it.
Many aquarists think water testing is unnecessary or a waste of money. The problem is the fish can appear healthy even though they’re swimming in toxic water.
It is quite normal for otherwise healthy-looking fish to be suffering from microscopic disease pathogens.
By the time the fish show signs of illness, it can be too late. Necropsy investigations on dead fish that looked healthy reveal diseased livers, kidneys and other organs.
This could have been prevented by checking on the water quality once every few weeks.


Water testing should be thought of as a preventative measure. No one is disappointed when the dental examine reveals no cavities. But aquarists sometimes think water testing is a waste of time when the tests show no problems. The idea is to catch declining water quality before it becomes a serious issue.
Aquarium water testing can be as easy as dipping a test strip into the water. In a matter of minutes, you’ll be able to see the status of ammonia, pH, nitrite, nitrate and more. It’s the responsible thing to do for your aquatic pets!

When draining the aquarium is a good idea

It’s rarely necessary or beneficial to drain, scrub and restart an aquarium after a disease outbreak.
If you follow the steps we’ve outlined your aquarium will recover nicely.

But there is a scenario when you’ll probably want to “nuke” the tank.

In situations where all the fish died and have reached a state of decay where bits of fish flesh are floating in the water, drain the aquarium! You’ll never be able to restore the aquarium through partial water changes and filtration. The oils from the dead fish will float on the surface.
Decaying fish stink! The particles of fish flesh will become trapped in the gravel and stick to the ornaments. Ammonia will rise as the rotting skin decays.


The only way put an end to all this is by draining the aquarium and washing everything.
Wash the gravel in a bucket until it rinses clean. Some aquarists choose to buy new gravel rather that handle the old material.
Wash the ornaments and filter system. Scrub the aquarium heater. Even the underside of the aquarium light can be coated with slime. You can use dish detergent or even dilute bleach.
Fish shops, universities and commercial fish farms use bleach and other powerful cleaners. That’s OK as long as the aquarium and equipment are thoroughly rinsed off after cleaning.
You can wash the aquarium down at the sink or bathtub. If you can carry it outside and use a garden hose, even better!

Final recommendations

There’s no reason to panic or take drastic measures after a bout with Ich or fin rot.
Just follow these tips and your aquarium will be healthy again. Reducing stress factors by proper aquarium care is the key to preventing disease problems. Some aquarists fail to learn this lesson and never have success with their tank.
But the truth is, sometimes even expert aquarists have to treat a sick fish. The good news is now you know how to take care of your aquarium after the treatment is over and the fish are well again.

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