How to Fix Unusual Odors in Hydroponics, Agriculture, and Water Tanks

What Causes Bad Smells in Water Systems?

1. Biofilm

Biofilm is a structured community of bacteria, fungi, and organic matter that attaches to pipes, tanks, roots, and surfaces. Once established, it acts like a protective shelter for microbes, making them resistant to flushing and many disinfectants. We have written extensively about biofilm, check out our articles here.

As biofilm matures, it:

• Traps organic waste

• Creates oxygen-depleted zones

• Produces volatile compounds responsible for musty, earthy, or sulfuric odors

Biofilm is often present long before you can see or smell it.

2. Low Oxygen & Anaerobic Activity

When dissolved oxygen (DO) levels drop, aerobic (beneficial) microbes lose dominance. Anaerobic bacteria take over and begin producing gases such as:

• Hydrogen sulfide (H₂S) → rotten egg smell

• Methane and organic acids → sour or stagnant odors

This commonly happens in:

• Stagnant zones

• Dead-end pipes

• Warm reservoirs

• Systems with poor circulation

Low oxygen doesn’t just cause smell — it directly harms roots and beneficial microbes. If you are not sure what's DO, we recommend you start with "What Is Dissolved Oxygen (DO) and Why It Matters for Water Health".

3. Decaying Organic Matter

Dead roots, algae, plant debris, bio-sludge, or excess nutrients provide food for microbes. As this material breaks down, it releases odorous byproducts.

Typical smells include:

• Fishy or sour notes → protein and nutrient decay

• Earthy or swamp-like smells → microbial decomposition

The more organic loading in your water, the faster odor issues develop.

4. Nutrient Imbalance & Overfeeding

Overfeeding nutrients or poor nutrient uptake creates a surplus in the water. This excess becomes fuel for microbial blooms, especially bacteria that thrive in warm, low-oxygen environments.

The result:

• Rapid biofilm growth

• Increased oxygen consumption

• Stronger and more persistent odors

How to Eliminate Odors — Systematically

1. Remove the Fuel: Organic Matter

Start with the basics:

• Remove dead roots, leaves, algae, and visible sludge

• Clean filters, sumps, pumps, and grow trays

• Inspect hidden zones where debris accumulates

Tip: Odor usually originates where water movement is weakest.

2. Reset the System with a Deep Clean

For systems already producing odors:

• Drain the system completely

• Mechanically clean accessible surfaces

• Disinfect the tanks, either with classical chemicals or ozone nanobubbles

• Rinse thoroughly to protect roots and microbes

This step removes existing biomass, but does not prevent regrowth on its own.

3. Microbial Control: Kill or Balance

There are two common approaches:

A. Oxidative treatment (short-term reset)

• Hydrogen peroxide breaks down odor-causing microbes and organic matter

• Provides a temporary oxygen boost

• Effective, but non-selective

B. Biological competition (long-term stability)

• Beneficial microbes (e.g. Bacillus species, EM cultures) outcompete harmful bacteria

• Requires stable oxygen levels to work effectively

Both methods fail if oxygen remains low.

4. Restore and Maintain Oxygen Levels

Oxygen is the central control variable.

• Increase water circulation

• Eliminate stagnant zones

• Use aeration or advanced oxygenation methods, our nanobubble generators maintain stable DO

• Monitor DO, especially in warm conditions

High and stable dissolved oxygen:

• Suppresses anaerobic bacteria

• Reduces odor formation

• Improves root health and nutrient uptake

• Slows biofilm regrowth

Also we recommend checking out our article about aerobic and anaerobic bacterias.

5. Improve Water Renewal & Filtration

• Perform regular partial water exchanges

• Use filtration to remove organic load

• Consider UV or carbon filtration for additional control

However, note: filtration treats symptoms — oxygen treats causes.

What If the Smell Keeps Coming Back?

Persistent odors usually mean:

• Biofilm is established inside pipes or emitters

• Oxygen never fully recovers

• Organic loading remains high

At this stage:

• Inspect internal plumbing and dead zones

• Test water for ammonia, nitrites, and microbial activity

• Consider a full system reset combined with improved oxygenation

A More Sustainable Approach: Preventing Odors at the Source

Instead of repeating clean → smell → clean cycles, modern systems focus on preventing anaerobic conditions entirely.

Advanced oxygenation methods, such as nanobubble technology, address the root causes by:

• Maintaining elevated dissolved oxygen without surface aeration

• Penetrating biofilm structures

• Reducing microbial odor production without chemicals or scrubbing

• Stabilizing water quality over time

This shifts odor control from reactive maintenance to continuous prevention.

Final Thoughts

Unusual odors are early warning signals of biological imbalance in your water system. They point to:

• Low oxygen

• Excess organic matter

• Microbial dominance shifts

• Biofilm formation

The most effective solution is not masking smells or frequent chemical cleaning — it’s creating conditions where odor-causing microbes cannot thrive.