Why Does My Blackwater Aquarium Smell? Understanding Anaerobic Bacteria and the Rotten Egg Odour

Hello readers, and welcome back to our Blackwater Aquarium Beginners Guide, your step-by-step resource to help you avoid common mistakes and build a thriving, balanced blackwater aquarium.

One of the most common questions we receive from beginners is:

“Why does my blackwater aquarium smell like rotten eggs?”

If your aquarium gives off a sulphur-like odour, do not panic. This is a very common issue during the early stages of setting up a blackwater aquarium and is usually caused by a natural process involving anaerobic bacteria.

What Causes the Rotten Egg Smell in a Blackwater Aquarium?

When you notice a smell similar to rotten eggs, it is typically due to hydrogen sulphide gas (H₂S), a by-product created by anaerobic bacteria. These microorganisms thrive in oxygen-deprived environments such as the soft, organic-rich substrate of a blackwater aquarium.

What Are Anaerobic Bacteria?

Anaerobic bacteria are microorganisms that live in environments with little or no oxygen. Unlike aerobic bacteria, which need oxygen to survive, these bacteria break down decaying organic matter through fermentation and other chemical processes. In blackwater habitats, they play an important role in recycling nutrients and maintaining ecological balance.

Key Anaerobic Processes in a Blackwater Aquarium

1. Decomposition of Organic Matter

When you add aquarium botanicals, driftwood, and leaves to create that natural blackwater look, they gradually decay and provide nutrients for various bacteria. Anaerobic bacteria break down these materials into simpler compounds, a natural process that helps form the tannin-rich, tea-coloured water that blackwater aquariums are known for.

2. Nitrate Reduction

In traditional aquariums, nitrates can build up and harm fish. In a blackwater aquarium, anaerobic bacteria help reduce nitrate levels by converting them into harmless nitrogen gas, which escapes into the atmosphere. This process helps maintain water quality and reduces stress on your fish.

3. The Sulphur Cycle – What’s That Smell?

This is where the distinctive rotten-egg smell comes in. During sulphate reduction, certain anaerobic bacteria convert sulphates found in the water into hydrogen sulphide gas (H₂S). While small amounts are normal in early stages, excessive build-up can create a strong odour and may cause pH instability if left unchecked.

Why the Smell Builds Up

When your blackwater aquarium has areas with low water flow or compact substrate, hydrogen sulphide gas can accumulate in small pockets. If you stir the substrate or disturb a piece of decaying wood, that trapped gas is suddenly released and your room quickly smells like rotten eggs.

It is unpleasant but not necessarily dangerous if addressed early.

How to Fix and Prevent the Rotten Egg Smell

1. Improve Air Supply

An air pump is a blackwater aquarium beginner’s best friend. It increases oxygen levels by disturbing the surface, supporting the aerobic bacteria, which help process waste before anaerobic bacteria can overproduce hydrogen sulphide.
Better oxygenation means better balance.

Beginner Tip: A lower pH slows the nitrogen cycle in blackwater tanks. Until you are confident managing water quality at low pH levels, keep an air pump running to help stabilise your nitrogen cycle and overall tank health.

2. Increase Water Flow

Adding a gentle current or upgrading your filter helps prevent stagnant zones. Improved flow limits areas where hydrogen sulphide can build up, reducing the chance of foul smells and maintaining a stable environment for your fish and aquarium botanicals.

3. Regular Maintenance

Perform small, regular water changes to maintain water quality.

• Use RO (reverse osmosis) water where possible.

• If you are using tap water, limit changes to around 10% weekly to avoid shocking your ecosystem.

• Clean debris from the substrate without disturbing too much of the biological balance.

4. Patience Pays Off

A new blackwater aquarium setup needs time to stabilise. The smell will fade as beneficial bacteria populations balance out. Avoid adding fish until the odour subsides. If the smell appears later in an established tank, increase aeration and check for decaying leaves or trapped waste.

Final Thoughts

If your blackwater aquarium smells bad, do not worry, it is part of the natural cycling process. A little tweaking of your water flow, air supply, and maintenance routine usually resolves it. Once stabilised, your tank will develop that beautiful amber hue and soft, earthy scent typical of a healthy blackwater ecosystem.

For more tips, explore our full Blackwater Aquarium Beginners Guide 101 and learn how to create a thriving, natural aquatic environment inspired by the Amazon rainforest.