Understanding Reef Tank Filtration: Biological Filters, Canister Filters, Protein Skimmers & Media Reactors

New England Aquaculture
Apr 21
3 min read

When it comes to reef tanks, think of them as life support systems for tiny pieces of the ocean. All that vibrant life brings waste—lots of it. And without proper management, this waste turns into harmful, even toxic compounds. Thankfully, nature has systems in place to handle this, and we can emulate those methods between water changes to keep our reef inhabitants thriving.

Biological Filters

Biological filtration is all about beneficial bacteria. Water flows through filter media that’s home to these bacteria, which consume the compounds in waste and either eliminate them or convert them into safer byproducts. Every biological filter—regardless of how it’s built—operates on this fundamental principle.

There are two main types of biological filters commonly used in reef tanks:

Wet/Dry Filters

These are classic systems used both by hobbyists and researchers. Water from the display tank is drained into the wet/dry filter—either directly or via a sump or manifold. From there, the water trickles or sprays over bio-media housed in a chamber (usually a box or tube).

Key points:

Bio-media provides surface area for beneficial bacteria.
Many systems include mechanical filtration using filter floss or pads.
If not included, a prefilter is essential to prevent detritus buildup.
Strong at biological filtration, but:
- Less efficient for chemical filtration.
- Activated carbon is usually used passively, reducing effectiveness.

Canister Filters

Canister filters address that shortfall. Like wet/dry systems, they use beneficial bacteria—but with the added advantage of a tower-like design that ensures water passes through mechanical, biological, and chemical stages in order.

Why they work well:

Compact and self-contained design.
Built-in pump and layered filtration.
Great for tanks up to 30 gallons that lack a sump.
Easy maintenance with monthly media replacement.
Effective and convenient for standalone reef systems.

Protein Skimmers

When tank size or bioload increases, wet/dry and canister filters alone aren’t enough. That’s where protein skimmers come in.

Protein skimmers (also known as foam fractionators) mix water and air in a reaction chamber, creating foam. Organic compounds bind to the bubbles and collect in a cup as a dense sludge.

Benefits:

Physically removes dissolved organic compounds from the water.
Helps manage nitrate and phosphate levels—common byproducts of biological filtration.
Effective even in smaller tanks.
Regular cup cleaning is required for optimal performance.

Media Reactors

Sometimes, high phosphate levels can persist despite solid biological filtration and protein skimming. Whether it’s from a heavy bioload, aggressive feeding, or untreated source water, phosphate can fuel unwanted algae blooms.

This is where media reactors—especially phosphate reactors—come in.

How phosphate reactors work:

Small chamber filled with plant-based polycarbonate media.
Gently tumbled by a pump to:
- Encourage bacterial colonization.
- Promote phosphate consumption during metabolism.
Bacteria produce phosphate-rich mucus, which flakes off during tumbling.
Waste is carried out and should be directed into:
- A mechanical filter chamber, or
- A protein skimmer for removal.

Final Thoughts

Filtration technology continues to evolve, with new designs and media hitting the market every few years. While it’s great to explore these innovations, beware of products that promise a “complete” solution. They often require micro-management or bring unrealistic expectations.

Instead:

Focus on understanding the specific needs of your tank.
Add filtration or use chemical treatments only when water changes aren’t enough.
Remember: Your reef's success is all about balance, thoughtful intervention, and continuous learning.

Get Expert Guidance with New England Aquaculture

Need help deciding on a filter type? New England Aquaculture offers Service and Consultation Plans to guide you in disease prevention, system design, and best practices. Contact us today to ensure the long-term success of your reef tank!