Why do algae keep coming back in your lagoon system? The 7 causes and how to get rid of them

You built a planted filtration bed specifically to avoid algae, yet it is covered in them. Green filaments between the gravel, a green film on the stones, water emerging less clear than it entered. It's frustrating, but it is also a valuable signal. Algae in a planted filtration bed almost always mean that the plants are not yet, or are no longer, absorbing all the nutrients entering the system. Finding out why is how you solve the problem for good.

How a planted filtration bed works, in two sentences

Pond water slowly passes through a planted gravel bed. Bacteria attached to the gravel and roots break down organic matter, while the plants absorb the released nitrates and phosphates to build their leaves. As long as the plants absorb more nutrients than enter the system, algae have nothing to feed on. As soon as the balance is reversed, they take hold, and the first place they often appear is the planted filtration bed itself, where the water arrives richest in nutrients.

The 7 most common causes

— 1. A planted filtration bed that is too young

In the first and second years, the plants have not yet developed their roots or foliage. Algae occupy the available space. This is normal, and it often resolves from the third season onward if the planting is dense.

— 2. Too small an area

A 1 m² planted filtration bed cannot purify a 20 m³ koi pond. For a natural swimming pond, professional recommendations call for a regeneration zone covering around half of the total area; for a lightly stocked ornamental pond, 20 to 30% is a realistic minimum. With fed fish, the planted filtration bed alone is generally not enough.

— 3. Clogged gravel

Without mechanical filtration upstream, sludge and debris accumulate between the gravel. Water can no longer pass through; it creates preferential flow paths, and the trapped material decomposes, releasing phosphates. A clogged constructed wetland becomes a source of nutrients.

— 4. Too much light on bare areas

Every square centimetre of gravel in full sun, without a plant, is an invitation for filamentous algae. A sparsely planted constructed wetland encourages more growth than a densely planted one.

— 5. Plants never harvested

Plants store nutrients in their leaves. If they are left to rot in place over winter, everything they have absorbed returns to the water in spring. Cutting and removing the biomass every autumn physically removes the nutrients from the system.

— 6. Excess phosphates

Phosphate-rich filling water, garden runoff, fallen leaves, fish food: phosphorus is the element that most often limits algae in fresh water. Just a few tenths of a milligram per litre are enough to feed them.

— 7. Unevenly distributed circulation

A poorly positioned drain or a single inlet creates dead zones where water stagnates and warms, as well as overloaded zones. Water must pass evenly through the entire bed.

The action plan

1. Increase planting density: 6 to 9 plants per m², mixing fast-growing and evergreen species.
2. Add mechanical filtration upstream (brush filter, sieve, prefilter) so the constructed wetland only receives water free of its particles.
3. Clear clogged areas: remove and wash the surface gravel, and vacuum up accessible sludge.
4. Remove algae by hand as they appear: each handful removed takes its nutrients with it.
5. Harvest the plants every autumn and remove them from the pond.
6. Limit phosphates: use a phosphate binder, test the filling water, and provide less food if you have fish.
7. Support the biology with bacteria that break down organic matter, especially in spring.

Read also

Plants for planted filtration and biological purification

READ THE ARTICLE

Frequently asked questions

— Should a planted filtration bed be treated with an algaecide?

This is not recommended. An algaecide also kills some of the beneficial organisms, and dead algae release their nutrients. It is better to remove the algae by hand and address their causes.

— How long does it take for a planted filtration bed to become effective?

Generally allow two to three seasons for the plants to become fully established. In the first year, additional filtration and a UV unit help you get through this stage.

— Does UV help a planted filtration bed?

It acts on algae suspended in green water, not on filamentous algae attached to the gravel. It can complement a young planted filtration bed, especially in a pond with fish.

— How deep should a planted filtration bed be?

Usually between 30 and 60 cm of substrate, covered by a few centimeters of water, so that the roots occupy the entire thickness through which the water flows.

In summary

• Algae in a planted filtration bed = more nutrients than the plants can absorb.
• Causes: young system, undersizing, clogging, light, phosphates, unharvested biomass.
• Solutions: plant densely, prefilter, unclog, harvest, limit phosphates.
• Patience: a planted filtration bed reaches full efficiency after two to three seasons.

Last updated: September 28, 2026.