If you have spent any time learning about aquaponics, you have probably heard the golden rule: keep your pH around seven.
The reasoning behind it is simple. Your system runs on a partnership between fish, plants, and bacteria — and these three ask for slightly different things. Plants prefer water a little on the acidic side, somewhere between 5.5 and 6.5. The nitrifying bacteria that keep your water safe prefer it slightly alkaline, around 7.5 to 8. So the advice has been to meet in the middle: pH 7. A compromise that satisfies nobody perfectly, but keeps everyone alive.
A 2024 study published in iScience suggests that this compromise is more flexible than we have been telling people — thanks to a group of bacteria we did not even know existed in 2015.
Let me walk you through what the researchers found, and what it actually means for the system in your backyard.
The nitrogen cycle, in one minute
Here is the short version of what the nitrifying bacteria do.
Your fish excrete ammonia. Ammonia is toxic — it will kill them if it builds up. A first group of bacteria converts that ammonia into nitrite. Nitrite is also toxic. A second group of bacteria converts nitrite into nitrate. Nitrate is safe for the fish and useful for the plants.
Ammonia → nitrite → nitrate. That is the nitrogen cycle. For decades, biologists thought that no single bacterium could do both steps. You needed two teams working in sequence. And both teams were understood to prefer slightly alkaline water. Hence the pH 7 compromise.
Comammox bacteria — the discovery we missed
In 2015, two research groups (Daims et al. and van Kessel et al., both in Nature) independently found something that overturned what microbiology textbooks had been teaching for a century. They described a bacterium that performs the complete ammonia oxidation in a single cell — not just the first step, but both steps. They called it comammox, short for “complete ammonia oxidizers”.
Comammox bacteria live in the same places we care about: biofilters, soils, lake sediments, and — crucially for us — the gravel and media beds of aquaponics systems. They tend to thrive in slower-growing, lower-ammonia environments. And they tolerate acidic conditions better than their classical counterparts.
That last point is the important one for anyone running a system with plants that prefer lower pH.
The 2024 study — what the researchers did and found
The study is Derikvand et al. (2024), iScience 27(3). The research group, based at the University of Alberta, had been working for years on an aquaponics microbial inoculum that stays efficient at acidic pH. This paper is the controlled test.
They ran two parallel aquaponics setups growing lettuce. One was held at the classical pH range, 7.6 to 7.8. The other was held between pH 5.8 and 6.0 — much lower than most aquaponics manuals would allow.
Three things were measured in both systems: what the bacteria did, how the plants grew, and how the fish held up.
What happened to the bacteria
In the pH 7.6-7.8 system, the usual nitrifying bacteria dominated — no surprise. In the pH 5.8-6.0 system, those bacteria were suppressed, but comammox took their place. Nitrite was removed effectively in both systems. In other words, the community rearranged itself but the job still got done. The researchers also did not detect ammonia build-up or dangerous nitrite spikes in the acidic system.
What happened to the lettuce
Lettuce in the lower-pH system produced more in every round of the experiment. The difference was not statistically significant across all trials combined, but the trend was consistent.
What happened to the fish
The goldfish in both systems were fine. No mortality, no visible stress.
A 2021 follow-up paper from the same group had already found that their inoculum retained about 81% of its nitrification activity at acidic pH, and produced no measurable nitrous oxide (N2O) — a greenhouse gas that conventional nitrifiers tend to release.
Four takeaways for your own system
I want to be careful here. This is one study. It does not say “run everything at pH 6”. It says the old compromise is more flexible than we thought. With that honesty on the table, here is how I would translate it for a backyard builder.
1. pH 7 is not a magic number
If your water naturally sits at 6.5, or 6.3, and your fish are healthy and your plants are growing — that is a working system. You do not need to fight it up to 7 with buffers and chemicals. Biology is more flexible than the old rule books suggested.
2. Change things slowly
The one thing that will kill fish faster than any specific pH is a sudden change in pH. A swing from 7.5 to 6.0 in a few hours stresses them even if 6.0 is otherwise fine. Give your system weeks, not hours. The bacterial community reshuffles slowly, and so should you.
3. Do not chase pH 7 with chemicals
Phosphoric acid, pH down, pH up, buffers — they all work briefly, and then your water bounces back, usually with a pH swing that is worse than where you started. Address the root cause (water source, substrate, biological activity) instead. A stable pH 6.5 is almost always better than an oscillating “pH 7”.
4. Biodiversity is your insurance
The lesson behind the 2024 study is bigger than pH. Systems with a diverse microbial community cope better with change. When one group of bacteria gets suppressed, another steps up. An aquaponics system is not a machine you control with numbers — it is a living ecosystem. The more alive and diverse it is, the more resilient it is.
The honest limits of the study
This was a single lab study. The fish were goldfish, not tilapia or trout. The plant was lettuce, not tomatoes or herbs. The duration was weeks, not seasons. Your mileage will vary. What this paper does not give us is permission to ignore everything we know. What it does give us is a well-controlled data point that the old pH 7 rule was never the whole story.
If you are new to aquaponics, do not start by trying to run your system at pH 5.8. Start the way most people start — around pH 7 — and get the basics right (cycle your system, stock gradually, feed sensibly). Once the system is stable and alive, let it settle where it wants to settle. If that happens to be 6.5, that is fine.
Watch the video
I walk through the study, the bacteria, and the takeaways on video — 8 minutes:
Want to go further?
If you want the full design framework I use to integrate water, fish, plants, and life into one space, it is in a free 13-page guide called The Oasis Plan. Backyard-focused, no fluff.
If you are new to aquaponics and want the foundations (nitrogen cycle, balance between fish, plants and bacteria, cycling your system correctly), Easy Aquaponics covers exactly that.
If you are ready to build a beautiful, integrated system that looks like it has always been there, Holistic Aquaponics is the flagship training.
Talk soon,
Jonathan
Sources
- Derikvand, P., Sauter, B., Keddie, N., & Stein, L.Y. (2024). Inoculum and pH effects on ammonium removal and microbial community dynamics in aquaponics systems. iScience, 27(3), 109073. https://doi.org/10.1016/j.isci.2024.109073
- Derikvand, P., Sauter, B., & Stein, L.Y. (2021). Development of an aquaponics microbial inoculum for efficient nitrification at acidic pH. Applied Microbiology and Biotechnology, 105, 5905-5917.
- Daims, H., Lebedeva, E.V., Pjevac, P., Han, P., Herbold, C., Albertsen, M., et al. (2015). Complete nitrification by Nitrospira bacteria. Nature, 528(7583), 504-509. https://www.nature.com/articles/nature15733
- van Kessel, M.A.H.J., Speth, D.R., Albertsen, M., Nielsen, P.H., Op den Camp, H.J.M., Kartal, B., et al. (2015). Complete nitrification by a single microorganism. Nature, 528(7583), 555-559. https://www.nature.com/articles/nature16459