3 Reasons for Rotten Ammonia Smell in Soil (9 Solutions)

For many reasons, an indoor herb garden is a delight. However, as it turns out, it’s the soil that can make any enthusiastic indoor gardener turn away in disgust. What causes soil to smell bad? Three things:

In general, soil can produce a rotten or ammonia smell because of insufficient oxygen due to the lack of drainage. This trigger the proliferation of a specific type of bacteria producing such smell. Also, the presence of underprocessed manure can be the cause of bad smell in soil.

But, no worries: the solutions are easy. 

This article will guide you keep your indoor herb garden healthy, growing well, and pleasing to all senses. 

Let’s start with a common problem: what to do when your soil smells like urine.

Sulfure Ammonia smell soil

Anaerobic Soil

According to Cornell University, plants like to consume nitrogen, phosphorus, potassium in soil, which is produced when compost (or fertilizer) breaks down. These components create a good smell of soil. 

So, when your soil begins to smell bad, that’s an indicator of anaerobic soil, which is soil that lacks oxygen. 

How is this a problem?

As we all know, plants breathe in carbon monoxide and breathe out oxygen. In anaerobic soil, plants can breathe in but not breathe out. Can you imagine how that feels? In addition, since they can’t produce root cells and tissue, their roots cannot absorb water. So, of course, your plant will die.

And what causes the bad smell? There are three possibilities.

My Plant Pot Water Smells Like Rotten Eggs


The USDA says that potted soil with a rotting smell like urine or ammonia indicates either poor water drainage or anaerobic soil. This can be caused by:

  • Moss: The soil contains moss that consumes all the oxygen. According to a report by Oxford Research Encyclopedia, it is the “upper green photosynthesizing portion of the moss that consumes oxygen.” 
  • Compacted soil: The soil is so tightly packed (practically solid, that is) that no air can exist in the plant’s roots area. Even when compacted soil is watered, it’s so dense that plants can’t breathe out. When oxygen levels are severely reduced in compacted soil, anaerobic bacteria thrive and produce “metabolites that can kill plant roots.”
  • Waterlogged soil: The soil has poor drainage and stagnant water does not allow air into the root area. A report by Derk Bakker of the Department of Agriculture and Food in Western Australia confirms that “when soil is so wet that “there is insufficient oxygen in the pore space for plant roots to be able to adequately respire,” gases such as carbon dioxide and ethylene gather and affect your plant’s root growth.

Thus, when soil smells like stale water, ammonia, sulphur, or rotten eggs, something’s decomposing in there. 

Fortunately, that’s easily fixed.


First of all, make sure that your soil contains at least 25% oxygen. Here’s how you can do it:

  • Remove moss and other oxygen-consuming life forms from the potting mix.
  • Break up the soil by adding organic matter, a little sand, and nutrients. Most important, avoid soil with high clay content. A compaction problem is solved by mixing improving porosity and drainage.
  • Dry up the soil: Waterlogged soil should be dried, and then add soil porosity by minimizing clay content and adding organic matter.
  • Control watering: If you have a drainage problem, clear holes in the pot to allow water to drain. If you think you’re overwatering, you’re probably right. Simply cut down on watering. Here’s a quick guide:
    • Water should be about ¼ of the pot’s size. 
    • If the soil feels damp, water a day or two later. 
    • Don’t water the plant if the drainage holes at the bottom feel damp.

Now, let’s take a closer look at the next problem: when soil smells musty, like swamp water or rotting vegetation.

Infested Soil

In indoor gardening, one visible symptom of soil infestation is root rot. The first signs are leaves turning yellow and the plant is wilting even if you’re watering regularly. 


If your potted plant’s soil smells like swamp water and the roots are mushy and dark, you have root rot, a plant disease caused by either overwatering or soil with fungal infection. 

This happens because too much water allows microbes, fungi, or bacteria to contaminate, breed, and consume all the oxygen in the soil. 


  • Diagnosis: Remove the plant from the soil. Feel the roots. If all roots look black and disintegrating or feel mushy, it’s too late. If some roots are firm and healthy, try and save the plant. 
  • Intervention: Use a pair of scissors to trim away the affected roots. Throw away the soil. Thoroughly wash the pot with a water and bleach solution. Let dry in the sun.
  • Treatment: Dip the remaining healthy roots in a fungicide solution (in case the root rot is caused by a fungus). 
  • Rehabilitation: Repot the plant in new soil. Make sure there is good drainage. 

PRO TIP: Don’t fertilize at the onset – this can shock your plant. 

Let’s look at another common problem: when your indoor garden soil smells like dried animal poo.

Raw Dung

If your potting mix smells like chicken manure or cow dung, that’s probably what creates a pungent odor that’s similar to ammonia. 


In mass-producing, potting mix, organic fertilizer is added to enrich the soil. This can include peat, moss, ground bark, chicken manure, and cow dung. Everything should be thoroughly processed by drying, aerating, and disinfection. 

However, when quality control fails, you get under-processed (raw) dung in your potting soil. The odor is produced when organic matter decomposes. In the process, gases that contain hydrogen sulfide and ammonia are released.

Another possible cause of an ammonia-like odor is the use of fertilizer or pesticide that contains ammonia-based components. For instance, bio-pesticides that smell bad may contain ammonium bicarbonate (chemical code 073401) or ammonium nonanoate (chemical code 031802), a substance that is toxic to humans


If you think the problem is overwatering, limit the water input or improve water drainage. Begin by allowing the soil to dry out before you water it again. 

On the other hand, if you’re not overwatering, examine the pesticide or fertilizer you’re using. 

  • Go green: If your pesticide contains ammonia-based elements, shift to greener products. 
  • Dry it out: If your potting mix has raw dung, decant the soil, and spread it out to dry in the sun, out in the open air, and downwind from you. (Take care that you don’t offend the neighbors.) 
  • Aerate it: The odor should go away after a few days of airing in the open. 
  • Change the soil: If that doesn’t work, throw the stinky soil away and restart with fresh soil. 

If the preceding answers don’t seem to work, no worries. The following solutions have been tried and tested. 

Six More Solutions

Soil Bad Smell Solutions Cinammon
  • Use cinnamon: You know how good cinnamon rolls smell, right? However, you may not know that cinnamon has been used to improve the smell of potting soil. It also prevents fungus infection. Careful use of cinnamon oil (it can burn the plant) is used to kill aphids and keep away bugs, spiders, wasps, earwigs, and silverfish.
  • Add baking soda: Baking soda is used to absorb odors in refrigerators, beds, curtains, and carpets. In indoor gardening, baking soda has been used to absorb odors and kill fungus in soil, stop powdery mildew, black spots, and other diseases on leaves. Insects hate it, too. PRO TIP: Use sparingly to avoid ion toxicity.
  • Apply hyssop or peppermint: The sharp scent of peppermint oil is cool and refreshing. Also, the earthy, woody scent of hyssop can be used to mask scents, repel insects such as vegetable mites, as well as to kill oxygen-consuming moss and help create aerobic soil. Careful: hyssop can be toxic to pets and humans.
  • Use non-synthetic zeolite: If it’s too difficult to bear the NH3 smell of fertilizer such as nitrogen, phosphorus, and potassium from manure, use zeolite, a natural, non-toxic agent that does not only mask but actually removes strong odors. And, wow: aside from many other benefits, zeolite in rock form is reusable indefinitely.
  • Add special clays: Other options include attapulgite and bentonite, which are types of clay popular for their superb odor-absorbing ability. In addition, bentonite also provides pesticide and disinfectant properties. Other options are kaolin and magnesium. PRO TIP: Always check for plant safety before use.
  • Don’t use soil: Many indoor herbs and vegetables can flourish without soil. In fact, popular herbs such as basil, sage, oregano, lemon balm, thyme, mint, ginger, and stevia can grow in water alone. 

Now, let’s take a quick look at one more problem: when the soil has no smell.

Effects of Sodium Bicarbonate (Baking Soda) on Plant Growth

Extra Problem: Soil With No Smell 

Your soil doesn’t smell, so you’re good to go, right?

Wrong. Very wrong.

Here’s what you should keep in mind: garden soil with no smell is not good for indoor plants.


The fact is, soil should have some kind of smell. For instance, soil with no smell indicates absence of rhizobacteria, endophytes, and epiphytes that are beneficial for plant growth. 

PRO TIP: Plant growth and development require bacteria that are known as Plant Growth-Promoting Rhizobacteria (PGPR) such as Azospirilla, Pseudomonas, Streptomyces diastatochromogenes, and Bacillus thuringiensis.   


When there’s no scent at all, something is out of balance. Here’s what you can do:

  • Read up on ways to balance the soil.
  • Check your potting soil’s nutrients.
  • Test to see if your soil has the right pH level.
  • Know how healthy soil looks and smells. 

Of course, the one surefire way to avoid stinky soil in your indoor herb garden is to use good soil in the first place.

But, if you’re just starting, how can you tell if you have the right kind of soil? 

One quick way: use your nose. The unique smell of soil is “because soil is not just dirt,” says Sheila Keeling in The Smell of Living Soil. In other words, good soil smells healthy. 

The question is: what exactly is the smell of healthy soil? 

That’s a great question – and here’s a great answer.

Have you ever smelled something from the soil after a rain or a thunderstorm? That’s the simplest way of experiencing what healthy soil smells like. 

More specific, healthy soil should smell “earthy, kind of sweet, not sour,” says a report quoting David Lindbo of the US Department of Agriculture.

Where Does the Smell of Rain Come From?

“Actually it’s not the soil we smell” but a chemical caused by soil-dwelling bacteria, Keeling explains. Here are three (3) key terms for you:

  • Petrichor: The smell of soil after it rains outside – or when a storm begins to wet the earth – is called petrichor. The name comes from a combination of the Greek words for stone (petros) and “the blood of gods” (ichor).
  • Geosmin and MIB: The pleasant petrichor aroma actually comes from gases released by bacteria and fungi, particularly Streptomyces, which produce geosmin and MIB (2-methylisoborneol). 

Yes, you can smell it. We humans can actually detect a drop of geosmin and MIB in a trillion drops of water. (Nerd fact: Camels are even better at it. That’s how they survive in dry deserts.)

Now you know almost everything about how healthy soil should smell and what to do with bad smelling soil. 

At this point, three practical questions come to mind. Let’s take a few seconds to answer them.

Frequently Asked Questions

Will any kind of topsoil work? It actually depends on what kind of topsoil is available to you. For indoor potting, soil that is light and airy enough to resist compaction should be used. 

Can you just go to any store and buy it? Only trusted or dependable providers of gardening materials should be visited.

Can you make potting soil yourself? Read up the the best type of soil for each plant. Don’t be afraid to experiment. 

  • For better nutrition and drainage, add 10 to 20% organic matter such as leaf mold, compost, or rich garden soil.
  • To create a lighter, more suitable growing medium for your herbs, experiment and find the best mix of topsoil and potting soil. 

And with that, we end this delightful read. 

But, wait.

Before you go, let’s not forget your three most important takeaways.

Summary of Rotten and Ammonia Smell in Soil

If you’re thinking of an indoor herb garden – or if you already have one – you know what to do when the soil begins to smell bad. 

At the same time, if anyone needs help, you can provide useful answers. For instance:

  • The good smell of soil: Healthy soil smells fresh and clean, earthy, and kind of sweet. One great example is the smell of the earth at the onset of rainfall.
  • The bad smell of soil: A bad smell indicates either anaerobic soil or soil that is contaminated with microbes, mold, fungus, moss or bacteria that can kill your plants.
  • Odors and solutions: There are different causes and solutions to bad soil odor: 
    • Waterlogging: Control watering or improve water drainage
    • Root rot: Decontaminate with bleach, rehabilitate with new soil
    • Raw manure: Aerate, replace the potting mix, or deodorize with zeolite, bentonite, attapulgite, essential oils, cinnamon, or baking soda.
    • No smell: Check for soil balance, nutrients, and pH level.

Congratulations, you’re now an expert on Soil Scents 101. 

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Happy gardening!

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