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Why does my fish tank smell? I cleaned it thoroughly!

by Catherine Tran 07 Aug 2023 0 Comments

What is that smell?

Is it coming from your aquarium?

OMG, the fish tank starting to smell 😱😱😱😱😱

If so, it could be a serious problem…

Recently while visiting a friend, I admired the fish in her aquarium.

However, I noticed it had an unpleasant smell. I asked her how often she had to clean, and she admitted, “I try to clean often, but lately it smells horrible and I don't know why.”

To help my friend and anyone else with this issue, I have looked into this issue and found the possible causes, the steps to identify the source, and the solution to remove and eliminate the bad smell.

A healthy aquarium will have a mild smell. I'm sure it's not a fishy smell. Instead, a pleasant smell. Here's how aquarists describe the scents in their tanks…

** Freshwater tank - Mild earthy scent, like freshly ploughed soil.

** Saltwater tank – A light, beach-like marine scent.



Hard to call it a bad smell, right? I mean, you can try to experience those scents.

Let's dig into more details to help you get rid of that nasty smell.

Why does my fish tank smell?


Your aquarium can stink for a number of reasons, but the most common causes are dead fish, rotting food, and excess fish droppings—possibly due to overcrowding.

Dead fish.

I had a pleco, they were kinda shy and only came out at night. They spend their time hiding in the corner of the tank. Days passed without me seeing them.

And then one day when I noticed a musty smell coming from the tank. Upon investigating, I discovered his decomposing body deep within his favourite hideout.

What a pity! But they didn't say a word to me before they decided to leave me 😭😭😭😭😭

The lesson I takeaway is: Be sure to check behind every rock, decoration and plant - places out of your sight. You'll be amazed at the tight spaces fish can get into.

Your dead fish may not even be in the tank! This often happens with jumping fish, such as killifish, which can easily jump out of an aquarium without a lid.

Needless to say, a fish out of the water won't be able to breathe for long… they will die and the worst part is the carcass will start to decompose and give off a terrible smell.

If your fish can jump, check the back of your aquarium stand and any nearby furniture for carcasses.

Your poor pet may have hidden in a hidden corner of the aquarium and died. If fish or their carcasses are in your tank, use a net to retrieve them. Be sure to clean the net after reuse.

For disposal, you can put it in a paper bag and throw it away, compost or bury it. If you choose to bury the fish carcass, be sure to choose a dry place and dig your hole at least 2 feet deep.

How to prevent odours caused by dead fish.

Unfortunately, this is the most difficult smell to control – no fish lasts forever. That is sad but true.

The best thing you can do is give your fish a long and healthy life by providing the right nutrients.

Good water quality, not stocking too many fish, proper diet and regular maintenance will greatly help your fish live a full life.

Feeding too much.

I know you don't want your fish to starve, but overfeeding is probably one of the worst things you can do to your fish. It can also be the cause of the horrible smell coming out of your aquarium.

You see… Your fish will only eat so much food in one feeding. Anything that is not eaten falls to the bottom of your aquarium and begins to rot.

When food goes bad, it releases gas, which causes a bad smell. The smell gets worse as the leftovers build up.

A good tank maintenance routine, such as cleaning the filter and using a gravel spacer, will remove most traces of rotting fish food and the odour associated with it.

How to prevent odours caused by too much fish food.


It's really simple – just give your fish the amount of food they eat in one session. This way, there will be no more fish food that causes unpleasant odours.

Figuring out how much to eat requires trial and error – with so many different fish species and many different types of fish food, the exact amount of food can vary considerably.

A general rule of thumb is to only feed the fish as much as they can eat in 5 minutes.

Fish droppings.

That bad smell can also be caused by the food your fish eat.

If your tank is stocked properly, you'll be doing your weekly maintenance long before manure starts to stink in your tank.

As you may know:

More fish = More bio-waste

Accumulation analysis quickly breaks down. When it does, it gives off a foul smell.

How to prevent odours caused by fish feces.

This is an easy fix! Don't put too many fish in your aquarium and only keep fish that are suitable for your sized tank.

Overstocking is a problem often encountered by beginners who don't know better.

Before you buy fish for your aquarium, consult with experts and store owners. They will give you the advice to make your first fish farming experience perfect!

However, if your aquarium is already overloaded and here are 2 ways you can deal with it:

  • Buy a bigger tank or resell some of your fish.
  • Sell it back to us.

At Micro Aquatic Shop, you are always welcome to resell fish that you do not need or simply want to exchange for money and buy other fish you like. Read more about the program HERE.

Rotten aquatic plant.


Dead plants are easy to spot. They no longer resemble their original appearance and often turn slimy brown or black.

Either way, you should remove dead plants as they also contaminate the water quality.

If your tree has only a few dead leaves, you may need to prune it lightly to remove the rotting parts.

And remember, algae are plants too. Algae can rot, leaving you with a horrible musty smell. Cyanobacteria can make your aquarium smell bad.

How to prevent odours caused by dead plants.

Keep them alive! Live plants do not give off odours.

I know, I know… Easier said than done. 

But by making sure the plants get enough light and nutrients, you'll give them the best chance to thrive in your aquarium.

Dirty filter.


In fact, it is not uncommon to find more rotting sludge in the filter than in the aquarium. After all, the job of a mechanical filter is to collect any debris floating in your aquarium and collect it in one place.

And because of this, the filters can have an unpleasant smell. Really bad!

How to prevent smell caused by your aquarium filter.


I'll be blunt – cleaning your filter should already be part of your regular maintenance routine…

When it's time to change the water, wash the filter media with the water you removed so it doesn't kill any good bacteria that are living on it. Doing so will remove most of the foul-smelling sludge from the joint.

Your substrate.

If the smell coming from your aquarium smells like rotten eggs, your substrate may be faulty.

The concept is quite complicated, so here's a beginner-friendly explanation:

Very fine sand or gravel that has compacted over time can create oxygen-free zones. When waste gets trapped in these bags, bacteria convert it into gas. Smelly gas!

This gas then rises through the aquarium and straight into your nostrils!

How to prevent your substrate from emitting smell.


Again, what is the name of this game?


A deep gravel vacuum or regular sand stirring can prevent these odorous air pockets from building up in your aquarium.

Before you choose a substrate for your aquarium, read how to maintain it!

Air conditioner.

The water conditioner you add during a water change can also cause your tank to smell bad.

Use my favourite moisturizer, Seachem Prime. There's no mistaking the egg smell that comes out when you open the bottle.

However, once you add conditioner to the water, the smell will quickly disappear to the point of being imperceptible.

How to prevent SMELLS caused by air conditioning water.

Avoid water conditioners with strong-smelling ingredients like sulphur, which is often the cause of rotten egg odours.

How to get rid of the smell

Before reading this step, make sure that you have identified the cause of the odour from the above.

If you do not eliminate the cause, the following methods will not fix the lingering odour.

STEP 1: Maintenance.

First, you want to clean your tank. Your aim is to remove every piece of rotting organic matter in your aquarium.

When trying to get rid of odours, I strongly recommend being more thorough than routine maintenance. So take the extra time to do the following:

** Cleaning glasses.

** Clean your substrate.

** Prune any dead leaves from the plant.

** Clean stones or decorations.

** Clean your input and output filters.

** Perform a partial water change.

** Rinse your filter to remove trapped trash.

… any other maintenance steps specific to your tank. If it looks like rotting scum and it doesn't belong in your tank, take it out!

If you haven't done maintenance for a while, chances are your tank will smell worse after you clean it.

The reason for this is that you are dislodging all the scum that is rotting, allowing them to float freely in the water. This should only be temporary. By monitoring your water quality with test kits and following a strict maintenance schedule, you will eliminate odours in no time.

But to speed up the process…

STEP 2: Change the water daily.

Over the next few days, perform a 10-15% water change. This will add clean, odour-free water to your aquarium while also removing some of the foul-smelling water.

STEP 3: Add a carbon filter (optional).

While you wait for the odour to go away, you can add a special ingredient to your filter to prevent odours from following their tracks…

When it comes to absorbing odours, activated charcoal works wonders. Also known as a carbon filter, this wonder substance draws odours from your water and prevents them from getting into your nose – it will also make your water clearer, eliminating discolouration.

The only downside is that the carbon filter needs to be replaced regularly, at least once a month. Once the carbon has absorbed all it can hold, the odour will return.





If you have made it this far, you may have noticed a pattern to prevent odours in your aquarium.

Did you notice it?


Perform proper and regular maintenance!

You see, almost all odours come from rotting organic matter. And with proper maintenance, these should be removed long before they build up and stink in your room.

So do yourself a favour and establish a maintenance routine. Your nose will thank you for it!

Do you have more odour-removal tips? Please comment below.

Micro Aquatic Shop - Aquarium Fish For Sale Near Me.

Unit 15, 2-8 Daniel Street, Wetherill Park, NSW 2164

Customer support: (02) 8320 3037

Email: support@microaquaticshop.com.au

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