Most people search for fish tank filtration when the water turns cloudy, fish start gasping, or a new tank won’t “cycle” properly. In nearly every case, the fix isn’t a miracle product—it’s matching the right filter to your tank, then maintaining it in a way that protects the bacteria doing the quiet, essential work.
A good filter doesn’t just polish the water. It stabilises the chemistry, keeps waste from rotting in the corners, and gives beneficial microbes the flow and oxygen they need to convert toxic ammonia into safer forms.1, 2
Why filtration matters (even when the water looks clear)
In a closed aquarium, fish waste, leftover food and decaying plant matter quickly become ammonia. Ammonia can harm fish at low levels, and it rises fast in an uncycled tank or after a filter failure.2, 3
Filtration is really three jobs working together:
- Mechanical filtration traps physical debris so it can be removed before it breaks down.
- Biological filtration grows nitrifying microbes on surfaces (especially inside the filter) to convert ammonia to nitrite, then nitrate.2, 3
- Chemical filtration uses media (such as activated carbon) to adsorb some dissolved chemicals, colours and odours—useful in specific situations, but not a substitute for cycling.4
The three filtration types, in plain terms
Mechanical filtration: catching the mess
Mechanical media acts like a sieve. It grabs suspended particles—uneaten food, plant fragments, fish waste—so they don’t keep circulating and dissolving into the water.5
Common mechanical options include:
- Sponge and foam (great all-rounders; also provide surface area for bacteria)
- Filter floss/pads (fine polishing, but clogs quickly)
- Pre-filter sponges on intakes (quietly effective, especially for canisters and HOB filters)
Mechanical filtration only helps if you remove the trapped waste. If media is left clogged and untouched, water flow drops and the trapped debris continues breaking down in the filter.5
Biological filtration: the living engine inside the filter
Biological filtration is where stability comes from. Nitrifying microbes colonise hard surfaces—filter sponges, ceramic rings, bio-media, gravel—and use oxygen-rich flowing water to convert:
This “cycling” process typically takes weeks in a new aquarium. During that time, ammonia and nitrite can spike unless you’re testing and managing the load carefully.2, 6
Chemical filtration: useful, but not always necessary
Chemical media is best treated as a tool you use on purpose, not a permanent requirement.
Activated carbon is commonly used to remove some dissolved organic compounds that cause yellowing, odours, and traces of medications. Standard activated carbon is not a reliable way to remove ammonia, nitrite or nitrate in an aquarium.4
Zeolite (in freshwater) can reduce ammonia by ion exchange. It’s often used temporarily during emergencies or in new setups, but it can become exhausted and needs regeneration or replacement, and it’s generally not used the same way in marine systems.7
Common filter styles (and what they’re good at)
Hang-on-back (HOB) filters
Easy to install and service, good for small to medium tanks. They usually combine mechanical and biological filtration, with optional chemical cartridges. Their strength is convenience; their weakness is limited media volume compared with canisters.
Canister filters
Strong flow, large media capacity, and flexible media layouts—ideal for medium to large aquariums. Because they hold plenty of biological media, they can be very stable once established (but they still need routine cleaning to prevent flow loss).
Sponge filters
Air-driven sponges are gentle and safe for fry, shrimp, and tanks with delicate fish. They offer excellent biological filtration for their size and simple mechanical capture, but don’t “polish” water as finely as a canister loaded with fine media.
Undergravel filters (less common now)
They can provide biological filtration by pulling water through the substrate, but they’re harder to maintain well, and they don’t suit all substrates or planted tanks.
How to choose the right filtration system
Choose filtration based on the realities of your tank, not the label on the box:
- Tank volume (more water usually means more waste capacity, but also more to circulate)
- Stocking and feeding (messy eaters and heavy stocking demand more mechanical capacity and stable bio-media)
- Fish behaviour (some species dislike strong current; others need it)
- Maintenance style (the best filter is the one you’ll actually service on time)
In practice, most healthy aquariums rely heavily on mechanical + biological filtration, with chemical media used only when there’s a specific reason (removing medication residues, tannin staining, or a known contaminant).5
Installation basics (quiet, steady, and safe)
Follow the manufacturer’s instructions for the specific unit, but these principles hold across most filters:
- Rinse new media (sponges, rings, floss) in dechlorinated water to remove dust.
- Set up for steady flow, not a sandstorm—aim the outlet so fish can rest away from the strongest current.
- Run the filter 24/7. Biological filtration depends on oxygenated flow; long stoppages can damage the biofilter.6
Routine maintenance that protects your biofilter
Most filtration problems come from one of two extremes: never cleaning the filter, or cleaning it so aggressively that the tank loses a chunk of its biological stability.
What to do (and what to avoid)
- Do rinse mechanical media when flow drops or the media looks visibly clogged.
- Do use aquarium water in a bucket during a water change to gently rinse sponges and pads, so you don’t shock the biofilm and you avoid exposing it to disinfectants.1
- Don’t replace all filter media at once unless you’re prepared for cycling instability afterwards.
- Don’t deep-clean everything on the same day (filter, substrate, decorations). Stagger big cleans to keep bacterial populations steady.
How often should you clean it?
There isn’t a single schedule that fits every tank. A lightly stocked aquarium may go weeks with minimal attention; a heavily stocked tank may need mechanical rinses far more often. Use these cues:
- Flow rate drops (often the first sign of clogging)
- Debris builds up in the water column after feeding
- Ammonia or nitrite appears on tests (treat as urgent)2, 6
Troubleshooting common filtration problems
Weak flow
- Check the intake for plant matter, snail shells, or a clogged pre-filter sponge.
- Rinse mechanical media (pads/floss clog fastest).
- Inspect the impeller well for sludge or grit.
Noisy filter
- Look for trapped air (common after cleaning or a low water level in HOB filters).
- Check the impeller for wear, misalignment, or debris.
- Make sure the unit sits level and isn’t vibrating against the tank or cabinet.
Cloudy water even with a running filter
- White haze can be a bacterial bloom in new tanks or after disruption—often improves as the system stabilises.
- Green water is usually free-floating algae; filtration helps, but light and nutrients drive it.
- Brown tint is often tannins from wood; activated carbon can help if you want the colour reduced.4
Ammonia or nitrite detected
This is a water-quality problem first, and a filtration problem second. Treat it as urgent: reduce feeding, do partial water changes, and check whether the filter has been stopped, over-cleaned, or clogged. Continue testing until ammonia and nitrite return to zero.2, 6
What proper filtration does for fish health and water clarity
When filtration is doing its job, the tank becomes quietly predictable. Waste doesn’t linger long enough to poison the water, oxygen remains steadier in the filter, and fish are less likely to be stressed by sudden chemical swings.2
Long term, stable filtration also means:
- fewer emergency clean-ups
- less equipment wear from constant clogging and overheating
- more consistent water test results, especially in established tanks6
Final thoughts
A healthy aquarium filter is mostly habitat: surfaces, flow, and oxygen. Mechanical media catches the visible waste. Biological media quietly processes the invisible toxins. Chemical media is optional—best kept for specific jobs, used thoughtfully, then removed when it’s done.4, 5
If your tank is struggling, start with the basics: confirm ammonia and nitrite are zero, restore steady flow, and maintain the filter gently rather than aggressively. Stability tends to return the way it arrived—slowly, then all at once.2
References
- RSPCA Australia Knowledgebase: How should I care for my tropical fish?
- RSPCA Australia Knowledgebase: Why is water quality important when setting up a fish aquarium?
- Microbial community succession of home aquarium biofilters associated with early establishment of comammox Nitrospira (peer-reviewed, via PubMed Central)
- Environmental Literacy Council: Does activated carbon remove ammonia from water?
- Aquarium filter (overview of mechanical, biological and chemical filtration)
- University of Florida IFAS Extension: Ammonia in Aquatic Systems
- Zeolite (including aquarium use and ammonia ion-exchange)
- NSW Department of Primary Industries: Yabby preparation for market (water quality notes on ammonia, nitrite, nitrate and biofiltration)
- Aquarium filter: Mechanical and chemical filtration (notes on trapped solids needing removal and common chemical media)
Veterinary Advisor, Veterinarian London Area, United Kingdom