Filtration is the backbone of every healthy reef tank. Corals, fish, and invertebrates all depend on clean, stable water, and your filtration system is what keeps that environment thriving. Understanding the basics will help you avoid common pitfalls like algae blooms, cloudy water, and stressed livestock.

Three Pillars of Reef Tank Filtration

1. Mechanical Filtration

Mechanical filtration removes visible particles from the water column—things like uneaten food, fish waste, and detritus. Common options include:

• Filter socks or cups – Catch larger debris; rinse or replace 2–3 times per week.
• Filter floss or pads – Great for polishing water; change frequently to prevent nitrate buildup.
• Roller mats – Automatic mechanical filtration that reduces maintenance for larger systems.

Tip: If your filter socks or pads smell strong or look brown, they’re overdue for cleaning. Dirty mechanical media can become a nutrient source rather than a filter.

2. Biological Filtration

Biological filtration is the heart of your reef system. Beneficial bacteria convert toxic ammonia into nitrite and then into less harmful nitrate. This process happens on every surface, but especially on:

• Live rock – A primary home for bacteria and microfauna.
• Bio-media – Ceramic blocks, spheres, or bricks with high surface area.
• Sand bed – Can support both aerobic and, in deeper areas, some denitrifying bacteria.

Never fully sterilize all your rock or bio-media at once. You’ll strip away the bacteria that keep your tank stable and risk an ammonia spike.

For a deeper dive into starting this process, see our guide on cycling a new reef tank.

3. Chemical Filtration

Chemical filtration targets dissolved compounds you can’t see, such as organics, phosphates, and metals. Common tools include:

• Activated carbon – Clears yellowing compounds and toxins; replace every 3–4 weeks.
• GFO (granular ferric oxide) – Helps reduce phosphate levels to combat nuisance algae.
• Resin blends – Target specific contaminants like ammonia or heavy metals.

Use chemical media sparingly at first. Over-stripping nutrients can stress corals just as much as high nutrients can.

Protein Skimmers, Refugiums, and Maintenance

Protein Skimmers

Protein skimmers are a staple in modern reef systems. They remove organic waste before it breaks down, improving oxygenation and water clarity. Aim for:

• A skimmer rated slightly above your total system volume.
• Regular cup cleaning (every few days) for consistent performance.
• Periodic pump and body cleaning to prevent calcium buildup.

If you’re deciding what equipment to prioritize, check our breakdown on essential reef tank equipment.

Refugiums and Natural Filtration

A refugium is a separate section of the sump or a dedicated tank where macroalgae and microfauna grow. It provides:

• Nutrient export – Macroalgae like chaetomorpha absorb nitrate and phosphate.
• Pod production – Copepods and amphipods thrive and feed your fish and corals.
• pH stability – Running the refugium light on a reverse schedule helps smooth pH swings.

Many hobbyists combine skimmers, refugiums, and chemical media for a balanced approach. The key is to test regularly and adjust slowly. For help dialing this in, read our article on managing nutrients in a reef tank.

Putting It All Together

A successful reef tank doesn’t rely on a single filter; it uses a layered system where mechanical, biological, and chemical filtration work together. Start with strong biological filtration, add reliable mechanical removal of waste, then fine-tune with skimmers, refugiums, and chemical media as your tank matures.

Keep your filtration simple, maintain it consistently, and let your test results guide any changes. With a solid filtration foundation, your reef will have the stability it needs to grow and display its full potential.

Sources

• Delbeek, J.C. & Sprung, J. The Reef Aquarium, Vol. 1–3.
• Fenner, R. The Conscientious Marine Aquarist.
• Holmes-Farley, R. “Reef Aquarium Water Parameters” and related articles, Reefkeeping Magazine.