What really happens at the bottom of a pond? Mud, bacteria, and gases explained

We look at a pond from above: the fish, the water lilies, the color of the water. Yet much of what determines its health takes place in the last few centimeters, where no one looks. When we plunge a hand into the sludge of a client's pond, the smell and color often tell the whole story of the past year. The bottom of a pond is a biological reactor in its own right: it recycles waste as long as it receives oxygen, and starts releasing nutrients and gases as soon as oxygen is lacking. Let's follow what happens, layer by layer.

The invisible rain that falls constantly

Every day, a pond receives a light rain of material: food scraps, waste, pollen, plant fragments, dead microscopic algae, dust and, in autumn, whole leaves. Limnologists call this sedimentation. It all slowly sinks and settles where the current is weakest: in corners, at the foot of planting shelves, and at the lowest point. That is why sludge is never distributed evenly. A glance at the bottom also tells you where your water circulation does not reach.

The workers at the bottom

This material does not remain inert. It is colonized by a very rich community: bacteria, aquatic fungi, protozoa, and then a whole range of small creatures that feed on them. Chironomid larvae (the famous red bloodworms), oligochaete worms, freshwater isopods, and mayfly larvae in the healthiest ponds. Together, they fragment, digest, and mineralize the waste. In a balanced pond, they are enough to recycle a good deal of what falls in. Bottom-feeding fish such as koi also benefit from this fauna by turning over the bottom.

A boundary just a few millimeters thick

Here is the point that few pond owners know. Wetzel describes it in his treatise on limnology: at the sediment surface, only a microzone a few millimeters thick remains oxygenated, sometimes less. Just below it, the oxygen has been completely consumed by decomposition. The mud is therefore divided into two superimposed worlds that function in entirely different ways.

When oxygen is lacking: the bottom switches sides

As long as the mud surface remains oxygenated, it acts as a lid. Oxidized iron binds phosphorus there, keeping it trapped in the sediments. But if the bottom water becomes depleted of oxygen (warm nights, still water, lots of decomposing matter), this film disappears. The iron becomes soluble and releases the phosphorus it was holding. Scheffer, in his work on shallow lakes, describes this mechanism of “internal loading”: the bottom feeds algae from within, even when nothing more is coming from outside.

This is why some ponds turn green every summer despite having a good filter and a new UV unit: the phosphorus comes from the bottom, not the fill water.

At the same time, sulfate-reducing bacteria produce hydrogen sulfide, which is toxic to fish even in small quantities, while methanogenic archaea produce methane. These are the bubbles that rise when you move a stone or plant a basket. Their presence is not a catastrophe in itself, but it indicates thick, poorly oxygenated sludge.

And what about the filter?

A biological filter works like an artificial pond bottom, but when properly managed: a highly porous medium, a permanent flow of oxygenated water, and bacteria that convert ammonia into nitrites and then nitrates. However, it only treats what the pump brings to it. Leaves and heavy deposits that remain on the bottom escape filtration and decompose where they lie. An oversized filter therefore cannot make up for a neglected bottom. Conversely, a healthy bottom greatly relieves the filter.

How to reactivate a tired bottom

The logic follows from the above. First, oxygen must be brought into contact with the sludge: an air diffuser placed at the lowest point creates an upward current that circulates the bottom water. Next, reduce the amount of material: remove leaves before they sink, vacuum accumulation areas, and do not overfeed. Finally, support decomposition with specialized bacteria, which work better in oxygenated sludge. These three measures reinforce one another; used alone, they produce disappointing results.

Read also

To choose how to oxygenate the bottom: Bottom aeration or surface aerator: which solution is best for a natural pond?.

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Frequently asked questions

— Why is the sludge in my pond black underneath?

Because it lacks oxygen. Iron and sulfur compounds formed without oxygen produce this dark color and rotten-egg smell.

— Are bubbles rising from the bottom dangerous?

They are mainly methane and other decomposition gases. They are not dangerous in themselves, but indicate thick sludge that should be reduced.

— Can the bottom turn the water green?

Yes. Oxygen-deprived sludge releases phosphorus into the water, a major nutrient for algae.

— Should all the sludge be removed?

No. A thin layer provides a habitat for beneficial organisms. The goal is to limit its thickness and keep its surface oxygenated.

In summary

• The bottom of a pond recycles waste through bacteria and small organisms.
• Only the first few millimeters of sludge remain oxygenated.
• Without oxygen, sludge produces gases and releases phosphorus that feeds algae.
• Oxygenating the bottom, reducing inputs, and aiding decomposition: the three levers work together.

Last updated: September 29, 2026.