How to clean an aquarium filter

The filter is the most important piece of the tank — it's where the nitrifying bacteria live that keep the nitrogen cycle running. Bad cleaning is the second most common way (after adding fish too early) that beginners kill their tank.

This guide covers what, when and how to clean inside the filter — for internal, hang-on-back, and canister filters. Plus: what to never do, even if the manual suggests it.

1. When the filter needs cleaning

Clean the filter when it starts working worse — not on a rigid calendar. Specific signs:

Flow has noticeably weakened (water comes out slower, fewer surface ripples).
Visible debris at the intake — brown sludge, plant debris blocking the strainer.
Filter is louder or vibrates (motor overloaded).
Rising NO₃ or cloudiness with unchanged feeding.

Rough schedule for a community tank with medium stocking:

Internal / HOB filter: rinse sponge every 3–4 weeks.
Canister filter: open and rinse every 2–3 months.
Mechanical floss (white pad): rinse weekly, replace every 2–3 months.
Ceramic / bio-media: never (unless it physically crumbles after years).
Activated carbon: replace every 3–4 weeks (if used).

2. What's inside the filter — media layers

To know what to clean, you need to understand why it's there. A typical filter has 3 functional layers:

Mechanical filtration (first from the water inlet)

What it is: coarse sponge, felt, or floss.
Role: catches waste, food scraps, leaves — large particles.
Behaviour: clogs fast, turns visibly brown.
What to do: rinse / squeeze regularly (in tank water), replace every few months as it wears.

Biological filtration (middle)

What it is: porous ceramic rings, bio-balls, sintered glass, bio-mat.
Role: home for nitrifying bacteria — this is where the nitrogen cycle happens.
Behaviour: looks pretty much the same externally for years. Internally full of bacteria.
What to do: DO NOT CLEAN AGGRESSIVELY. Gently rinse in tank water once every six months. Never replace all of it at once.

Chemical filtration (last, optional)

What it is: activated carbon, Purigen, peat, phosphate/nitrate removers.
Role: binds dissolved substances (tannins, medications, excess organics).
Behaviour: loses capacity after 3–4 weeks.
What to do: replace with fresh, don't rinse.

Note: not every filter has all three. Simple internal filters often only have a sponge (mechanical + biological in one). Canisters have the full range.

3. The golden rule: never under the tap

Don't rinse filter media under the tap. Ever. Under no circumstances. Even if the manual says so, even if it's "just a second".

Why: tap water contains chlorine and chloramines — disinfectants. They kill nitrifying bacteria in minutes. The result of this "laundering":

A mini nitrogen cycle for 5–10 days.
Spikes in ammonia and nitrite (you'll see in tests).
Stress, lethargy, sometimes dead fish.
Bacterial bloom (white cloudiness) as a side effect.

The right way: in tank water

During your weekly water change — set aside some of the siphoned water in a bowl (2–3 L is enough).
Take out the filter media.
Gently squeeze them in the bowl. The water turns brown — that's fine.
Repeat 2–3 times until the bowl is less filthy (doesn't need to be crystal clear).
Put the media back in the filter.
Dump the dirty bowl water down the drain — not back into the tank.

Takes 5 minutes. No chlorine, bacteria survive, filter keeps working.

4. Step by step (HOB filter)

HOB (hang-on-back) is the most common type for 50–150 L tanks. Universal procedure:

During a water change — don't squeeze this into "I have 10 minutes before I leave". Do it calmly.
Prepare a bowl with tank water (2–3 L).
Unplug the filter (safety + reveals whether the sponge is actually blocking flow).
Take out media one by one — usually sponge + floss + optional bio-media (ceramic).
Sponge — squeeze 2–3 times in the bowl. That's enough.
Floss — if very dirty, toss it and put in a new one. If moderately dirty — rinse and keep.
Ceramic / bio-media — leave it alone! Unless covered in a thick mud layer, then gently shake in the bowl.
Filter housing — quickly wipe the outside with a damp cloth. Don't touch the inside.
Motor impeller — take it out, check it. If plant strings or snails block it — clean gently with a toothbrush. Every 6 months.
Reassemble in reverse order, plug in, check it's priming (sometimes you need to "prime" the tube).

5. Canister filter — different approach

Canisters are larger, have more media, and are cleaned less often — every 2–3 months. Procedure:

Close the valves on the hoses (if the model has them — most do).
Disconnect the filter from the tank.
Move to the bathroom (or kitchen — anywhere with a drain). A full canister weighs several kilos.
Open the canister (model-dependent — some have latches, some clips).
Pour out the old water (into a drain, not back into the tank).
Mechanical media (coarse sponge, fine sponge, floss) — rinse in a bowl of tank water, as above.
Biological media (ceramic, bio-balls) — leave alone. Maybe a gentle shake.
Canister housing — wipe inner walls with a sponge. The motor head can go under the tap (it's outside the biological zone).
Motor impeller — pull out, clean under tap, check the shaft (any cracks, does the impeller spin freely).
Seals — inspect for cracks. If the filter is 3+ years old — worth replacing seals proactively.
Reassemble, reconnect, plug in — some models need priming (suction or a priming button).

Key: don't clean everything at once. If you have 4 sponges — wash the 2 dirtiest. Next month the other 2. This preserves the bacterial colony's continuity.

6. Internal (sponge / submersible) filter

The simplest type — usually just a sponge and motor. Procedure simpler than above:

Unplug.
Take the whole filter out of the tank (water will leak — have a bucket ready).
Unscrew the sponge from the motor.
Squeeze the sponge 3–4 times in a bowl of tank water.
The motor can be rinsed under the tap; check and wipe the impeller.
Reassemble, put back, plug in.

Frequency: internal filters clog faster (less capacity) — every 3–4 weeks.

7. When to replace media

Mechanical media (sponges, floss)

Coarse sponge: replace every 12–24 months, or when it falls apart when you squeeze it. Replace one at a time, not all at once.
Fine sponge: every 6–12 months.
Floss (white pad): every 2–3 months, faster with digging fish or heavy stocking.

Biological media (ceramic, bio-balls)

Practically never — until it physically crumbles. Bacteria colonise ceramic deep into the pores; replacing = resetting the cycle. If you must replace:

Replace 1/3 at a time, never everything.
Keep the old alongside the new for 2–3 months (bacteria "migrate").
Monitor NH₃ and NO₂⁻ for 2 weeks after replacement.

Chemical media

Activated carbon: every 3–4 weeks. After that it "saturates" and may start releasing bound substances back.
Purigen: after it "browns" — regenerate in a 1:1 bleach solution for 24 h, rinse with conditioner, return to filter. Reusable.
Phosphate / nitrate absorbers: replace when parameters stop dropping despite use.

8. Common mistakes

1. Cleaning under the tap

Number one on the list. Already covered. Never.

2. Replacing all media at once

Classic trap: "once a year I'll deep-clean everything". Result — dramatic drop in bacterial population, mini-cycle, sick fish. Stagger replacements over time.

3. Aggressive cleaning of biological media

Ceramic is supposed to look brown. That's not dirt — those are bacteria. Don't scrub, don't rinse aggressively, don't put it in an ultrasonic cleaner (I've seen that advice on forums — don't).

4. Cleaning too rarely

The other extreme. A clogged filter has weak flow, accumulates sludge, smells bad, and lowers oxygen. If you haven't cleaned in months — expect a bacterial bloom, cloudy water, excess nitrate.

5. Priming the filter with tap water after cleaning

A canister needs to be "primed" with water so the pump starts. Some people use tap water. That drops chlorine right onto the bio-media. Prime with tank water (from the water-change bucket).

6. Ignoring the impeller

The motor impeller collects snails, plant strings, small grains. Blocked impeller = noise, vibration, burned motor in 6 months. Every six months, pull it out, clean with a toothbrush.

7. Swapping to a new filter without transferring media

If you swap to a bigger filter, move the old media (sponge, ceramic) into the new filter, even if they look "ugly". Starting a new filter with totally fresh media = cycling all over again.

9. If the filter crashed (bacterial bloom)

Suppose you made a mistake — rinsed under the tap or replaced everything at once. Now what?

Test NH₃ and NO₂⁻ daily for 7–10 days.
30% water changes every 2 daysif ammonia / nitrite > 0.
Seachem Prime dosed every 24 h — temporarily detoxifies ammonia and nitrite. Available at any aquarium shop.
Halve feeding until parameters stabilise.
If you know someone with a mature filter — borrow a sponge for a week. It'll seed the missing bacteria.
Bacterial starters (Tetra SafeStart, API Quick Start, Seachem Stability) — sometimes help, no guarantees.

More on dealing with cloudy water after such a crash in our cloudy water guide.

10. FAQ

Do I need to unplug the filter to clean it?

Yes, for two reasons: (1) safety — a running motor with the filter disassembled risks burning the pump, (2) you see the actual flow state when it's off — a quick restart after switching on confirms everything is fine.

How long can the filter be off?

Up to 30 minutes — safe. Over 1 h — water inside the filter loses oxygen and bacteria start dying. If cleaning takes longer (e.g. a canister with 5 media layers), pull out the bio-media and keep it in a bowl of tank water — don't leave it in the filter with no flow.

Can I run two filters in one tank?

Yes — and it's a great setup. If you have to replace a filter (e.g. old one broke), the second keeps the cycle running. Alternatively: canister as the main + a small internal as a "backup".

What do I do with the old filter after buying a new one?

Loan it to a friend's new tank (or your own, if you have one) for 2–4 weeks. A mature sponge is the single most effective cycling tool — someone needs it.

My filter still isn't pumping water after an hour. What happened?

Most common causes (by likelihood): (1) air in the tube — prime again, (2) impeller inserted backwards, (3) clogged intake, (4) closed valve, (5) damaged impeller. Check in that order.

Should I swap all sponge media for ceramic?

For a typical tank — sponge + floss + a bit of ceramic is the standard and plenty. Ceramic isn't intrinsically "better" — it does the same biological job, and you need mechanical filtration (sponge) anyway.

Can I turn the filter off at night for quiet?

No. After 12 h nitrifying bacteria start dying (no oxygen). Alternatives: buy a quieter filter (a canister has a virtually silent motor) or regularly lubricate the impeller.

What about the fish during cleaning?

Leave them in the tank. Cleaning the filter won't hurt them — it takes 5 minutes, and millions of bacteria in the tank stay on decorations, substrate, and glass. Even with the filter off for 30 minutes, fish are safe.

Wrap-up

A good filter cleaning routine:

Always in tank water — never under the tap.
Mechanical sponge every 3–4 weeks, canister every 2–3 months.
Leave biological media alone — only a gentle rinse once every six months.
Replace floss, practically never replace ceramic.
Check the impeller every six months — with a toothbrush.

If you've already made a mistake (tap water, replaced everything at once) — 30% water changes every 2 days, Seachem Prime, patience. The cycle rebuilds in 1–2 weeks if you stop panicking and don't make more mistakes.

Related: nitrogen cycle (understand what bacteria do in the filter), cloudy water (what to do after a bad cleaning), water changes (the natural moment to clean).