Reef Filtration Basics

Jan 11, 2026

If you want thriving corals, clear water, and healthy fish, you need to understand reef filtration basics. Good filtration does far more than just make the tank look clean; it keeps ammonia and other toxins in check, stabilizes pH, and supports the delicate biology that makes a reef system work.

The Three Pillars of Reef Filtration

1. Mechanical Filtration: Trapping the Gunk

Mechanical filtration physically removes particles from the water: uneaten food, fish waste, and detritus. Common options include:

Filter socks – Great at polishing water but need to be changed every 2–3 days.
Filter floss or pads – Cheap and easy to swap out; perfect for sumps and hang-on-back filters.
Roller mats – Automated mechanical filtration that constantly advances clean media.

Rinse or replace mechanical media regularly. Letting it sit and rot in the sump just turns it into a nutrient factory. Pair this with a consistent maintenance routine, like the one outlined in our reef tank maintenance checklist, to keep detritus under control.

2. Biological Filtration: The Bacteria Engine

Biological filtration is the heart of a reef system. Beneficial bacteria convert toxic ammonia to nitrite and then to less harmful nitrate through the nitrogen cycle. Key surfaces for this bacteria include:

Live rock or quality dry rock – The primary home for nitrifying bacteria.
Bio-media (blocks, balls, bricks) – High surface area options that boost capacity in smaller sumps.
Sand beds – Shallow beds provide some filtration; deeper beds may host denitrifying bacteria if carefully managed.

Give your tank time to cycle before adding a full fish load, and avoid over-cleaning surfaces. Scrubbing everything sterile can crash your bacterial population. If you are starting a new system, pair this with our guide on setting up your first reef tank to plan rock and media from day one.

3. Chemical Filtration: Fine-Tuning Water Quality

Chemical filtration targets dissolved compounds that mechanical and biological methods miss. Common tools include:

Activated carbon – Removes discoloration, odors, and some toxins.
GFO (granular ferric oxide) – Helps control phosphate, which fuels algae.
Resins – Target specific issues like ammonia, organics, or heavy metals.

Run chemical media in a reactor or high-flow area of the sump. Change it on schedule; exhausted media can leach what it absorbed back into the water.

Putting It Together: Practical Filtration Setups

A simple, effective reef filtration layout might look like this:

Overflow to filter socks or roller mat (mechanical)
Protein skimmer chamber (mechanical & organic removal)
Bio-media and live rock in the sump (biological)
Media reactor with carbon and/or GFO (chemical)
Return pump back to display

Tip: Size your filtration for the tank you want, not just the tank you have. If you plan to upgrade, choose a skimmer and sump that can handle the future volume.

Don’t forget natural methods, too. A refugium with macroalgae can export nutrients and stabilize pH. For more on balancing nutrient export, check out our article on controlling nutrients in reef tanks.

Final Thoughts: Balance Over Brute Force

Reef filtration isn’t about cramming in every gadget; it’s about balance. Combine reliable mechanical, biological, and chemical filtration, then support it with regular water changes and testing. When your filtration is tuned correctly, you’ll notice fewer algae issues, more stable parameters, and livestock that simply looks better and behaves more naturally. Start with these basics, adjust slowly, and let the tank’s long-term stability be your guide.