Brown Algae in a New Aquarium: What It Is and How to Fix It

What Is Brown Algae? (It Is Not Actually Algae)

The brown, dusty coating covering the glass, substrate and decorations in your new aquarium looks like algae, but it is not. What most aquarists call “brown algae” is actually a bloom of diatoms — single-celled organisms with silica-based cell walls. Diatoms belong to a completely different biological group from true algae, though the distinction is largely academic for most hobbyists. What matters is understanding why they appear and how to deal with them. This guide sits inside our broader Freshwater Aquarium Complete Beginner Hub reference.

Diatoms form a thin, brown film that wipes off easily. Unlike many true algae species that grip surfaces tenaciously, diatom films are loosely attached and can be removed with a gentle swipe of your finger, a cloth, or an algae scraper. They coat everything indiscriminately — glass panels, plant leaves, substrate, rocks, driftwood, filter intakes and equipment.

If you have just set up a new aquarium and noticed this brown coating appearing within the first few weeks, take a breath. This is one of the most normal things that can happen in a new tank.

Why Diatoms Appear in New Aquariums

Diatoms thrive in new tanks because the conditions are perfect for them and the competition that would normally suppress them has not yet established itself.

Silicates in New Substrate and Tap Water

Diatoms are unique among aquatic organisms because they build their cell walls from silica (silicon dioxide). New substrates — whether gravel, sand or aqua soil — often release silicates as they settle in. Singapore’s PUB tap water also contains dissolved silicates. In a new aquarium, these silicates are abundant and largely uncontested, providing the building blocks diatoms need to multiply rapidly.

Immature Biological Balance

A new aquarium lacks the established microbial community that keeps organisms like diatoms in check. In a mature tank, beneficial bacteria, competing algae, and microorganisms occupy every available niche. In a new tank, diatoms face little competition and can colonise surfaces freely.

The Nitrogen Cycle Connection

Diatom blooms often coincide with the tank’s cycling phase (the first 4-8 weeks). During this period, ammonia and nitrite fluctuate as beneficial bacteria populations establish themselves. These nutrient fluctuations, combined with available silicates, create ideal conditions for diatom growth.

Low Light Levels

Interestingly, diatoms are more competitive in low-light conditions than many true algae species. Beginners who keep their lights low or run them for short periods (hoping to avoid algae) may inadvertently favour diatoms over beneficial green algae and plants that would otherwise outcompete them.

Timeline: How Long Does It Last?

In the vast majority of cases, diatom blooms in new aquariums are self-limiting. Here is what to expect:

Phase	Timeframe	What Happens
Onset	Week 1-3	Brown film begins appearing on glass and substrate
Peak	Week 3-5	Diatoms at their worst — everything coated in brown film
Decline	Week 5-8	Diatoms gradually thin out as silicates deplete and competition increases
Resolution	Week 6-10	Diatoms largely disappear, replaced by a more balanced microbial community

Most hobbyists see significant improvement by week 6 and complete resolution by week 8-10. The timing varies depending on silicate levels, light, plant mass and whether algae-eating organisms are present. In some tanks, diatoms disappear within 3-4 weeks; in others, they linger for up to 12 weeks. Patience is the key.

Manual Removal Methods

While diatoms will resolve on their own, manual removal keeps your tank looking clean during the transition and prevents excessive buildup on plant leaves (which can block light).

Glass Cleaning

Diatoms wipe off glass easily. Use an algae scraper, magnetic glass cleaner, or even a clean microfibre cloth. For acrylic tanks, use a soft pad — abrasive scrapers will scratch the surface. Clean the glass every few days during the peak phase.

Substrate Siphoning

During water changes, hover the siphon just above the substrate surface to vacuum up the brown film. Do not plunge deep into the substrate — you want to remove the surface diatoms without disturbing the substrate bed. This is particularly effective for sand substrates, where diatoms settle in a visible layer on top.

Plant Leaf Cleaning

Gently wipe diatom film from broad-leaved plants (Anubias, swords, Cryptocoryne) using your fingers or a soft brush. For delicate plants, a gentle swish in the water current during a water change can dislodge loose diatoms. Removing diatoms from leaves is more than cosmetic — the brown film blocks light and can slow plant growth, which in turn delays the establishment of the plant mass that will outcompete the diatoms long term.

Decoration Cleaning

Remove heavily coated rocks and driftwood and scrub them under running water (tap water is fine for hardscape, as it will be rinsed before returning to the tank). This provides immediate visual improvement.

Algae Eaters That Devour Diatoms

Certain algae-eating species are exceptionally effective at consuming diatoms. Introducing them once your tank is cycled can significantly shorten the diatom phase.

Otocinclus (Oto Catfish)

The undisputed champion of diatom removal. Otocinclus catfish (Otocinclus affinis and related species) are small, peaceful, and have an insatiable appetite for diatoms. A group of 4-6 in a 60-100 litre tank can clean diatom-coated surfaces within days. They are gentle on plant leaves and will not damage even delicate species.

Important caveats:

Otos are sensitive to water quality — do not add them to an uncycled tank
They need diatoms or biofilm to feed on; once diatoms are gone, supplement with blanched vegetables (courgette, cucumber) or algae wafers
Always keep them in groups of at least 4 — they are social fish that stress when kept alone
Acclimate carefully; they are sensitive to parameter changes

For more on keeping these wonderful little fish, see our Otocinclus care guide.

Nerite Snails

Nerite snails are tireless grazers that work around the clock, scraping diatoms from glass, rocks and decorations. They are arguably the best glass cleaners in the hobby. Available in various attractive patterns (zebra, horned, olive), they are a functional and decorative addition. Nerites cannot reproduce in freshwater (their larvae require brackish water), so you will not end up with a snail population explosion.

Amano Shrimp

Amano shrimp (Caridina multidentata) consume diatoms along with other forms of biofilm and algae. They are less effective than Otocinclus for pure diatom removal but are excellent general-purpose cleaners. Hardy and easy to keep, they tolerate Singapore’s warmer temperatures better than some other shrimp species.

Bristlenose Pleco (Ancistrus)

A small pleco species (growing to about 12-15 cm) that grazes on diatoms and other surface algae. Suitable for tanks of 80 litres or larger. They are more robust than Otocinclus and continue eating various forms of algae and biofilm throughout their lives, making them a long-term algae management solution rather than a diatom-specific one.

Light Adjustments

Counterintuitively, increasing light can help combat diatoms. Here is why: diatoms thrive in low-light conditions where true green algae and plants cannot compete effectively. By providing moderate to strong lighting (and matching it with adequate plant mass), you favour plants and green algae that will outcompete the diatoms for nutrients.

Recommendations:

Run your lights for 8-10 hours per day on a consistent schedule
Ensure light intensity is appropriate for your plant species (not too dim)
If you have a dimmable light, start at 60-70% intensity during the first weeks, then increase gradually
Combine increased light with fast-growing stem plants or floating plants to establish a competitive plant mass quickly

Avoid the temptation to reduce light duration or intensity in response to diatoms — this often makes the problem worse by weakening the plants that would otherwise outcompete them.

When It Is NOT New Tank Diatoms

If brown coatings persist in a mature tank (older than 3 months) or reappear after initially resolving, the cause may be something other than new-tank diatom bloom:

Ongoing Silicate Source

Some substrates continue to leach silicates for extended periods. Certain types of sand, particularly play sand or pool filter sand, can be significant silicate sources. If your substrate is providing a continuous supply, diatoms will persist. Solutions include switching to an aquarium-specific substrate or using a silicate-removing filter media.

High Silicates in Tap Water

If your tap water contains elevated silicates, every water change reintroduces them. Using RO water for water changes and top-offs eliminates this source entirely. A silicate test kit (available from some aquarium shops) can confirm whether your tap water is the issue.

Low Light in a Planted Tank

A mature planted tank that has had its light replaced with a weaker one, or one where plant growth has declined (reducing nutrient uptake), can experience a diatom resurgence. Re-establishing strong plant growth is the long-term solution.

Persistent Brown Algae vs Diatoms

True brown algae (Phaeophyta) does exist in freshwater aquariums but is far less common than diatoms. If the brown coating is stubborn, does not wipe off easily, and has a more fibrous or slimy texture (rather than the powdery feel of diatoms), it may be a different organism. For persistent algae issues in mature tanks, see our comprehensive algae removal guide.

Prevention Tips

While diatoms in a new tank are largely unavoidable, you can minimise their severity and shorten their duration:

Use aquarium-specific substrates: Quality aqua soils and aquarium-grade sands are processed to minimise silicate leaching compared to generic substrates.
Plant heavily from day one: The more plant mass you start with, the faster plants establish dominance over the nutrient pool. Fast-growing species like Hygrophila, Rotala and floating plants are excellent for this purpose.
Add algae eaters once cycled: Introduce Otocinclus or nerite snails as soon as your tank is cycled and parameters are stable (typically week 4-6). Their grazing dramatically accelerates diatom removal.
Maintain good lighting: Provide appropriate light intensity and a consistent 8-10 hour photoperiod from the start.
Keep up with water changes: Regular water changes during the cycling phase remove dissolved silicates and excess nutrients that fuel diatom growth.
Consider RO water: If your tap water is particularly high in silicates, using RO water for initial fills and water changes removes a major diatom fuel source.

Frequently Asked Questions

Are diatoms harmful to fish?

No. Diatoms are harmless to fish, shrimp and snails. They are unsightly but pose no health risk to your livestock. In fact, some fish and invertebrates (particularly Otocinclus, nerite snails and shrimp) actively feed on diatoms as a food source. The only concern is heavy diatom coating on plant leaves, which can block light and slow plant growth.

Should I do extra water changes to get rid of diatoms?

Regular water changes (20-30% weekly) are beneficial during the new tank phase for overall water quality, and they do help by removing some dissolved silicates. However, aggressive or excessive water changes are not necessary specifically for diatoms. The bloom will resolve itself regardless. Focus on maintaining normal maintenance routines rather than reacting with panic water changes.

I have diatoms and green algae at the same time. Is this normal?

Yes, and it is actually a good sign. The appearance of green algae (particularly green dust algae on glass or green spot algae on slow-growing leaves) often signals that the tank’s microbial community is maturing. Green algae species are competitors that eventually displace diatoms. As plant mass increases and the biological balance matures, both should come under control.

Will adding chemicals or algaecides remove diatoms?

We strongly advise against using chemical algaecides in a new tank. The biological balance is still establishing itself, and introducing chemicals disrupts this process. Algaecides can also harm plants, invertebrates and beneficial bacteria. Diatoms resolve naturally — there is no need for chemical intervention. The best “treatment” is patience, manual removal, and the introduction of algae-eating organisms once the tank is cycled.

Brown diatom blooms are a rite of passage for every new aquarium. Understanding that they are temporary and harmless makes the experience far less stressful. If you are setting up a new aquarium and want expert guidance from day one — including planted tank design, cycling support and ongoing maintenance — visit Gensou at 5 Everton Park or contact our team. With over 20 years of experience, we have helped countless Singapore aquarists navigate the new tank phase and build thriving, beautiful aquariums.

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