Filter Systems Basics

Filter Systems for a Healthy Saltwater Aquarium

Choosing the right filter system is one of the most important decisions you’ll make in the saltwater aquarium hobby. Good filtration keeps water clear, stable, and safe for fish and corals, while poor filtration leads to algae blooms, stressed livestock, and constant frustration. In this guide we’ll break down the main types of filtration, how they work together, and how to choose the right setup for your reef or fish-only tank.

The Three Pillars of Filtration

Every effective filter system in a saltwater aquarium supports three basic types of filtration: mechanical, biological, and chemical. Most hobbyists use a combination of all three.

Mechanical Filtration: Trapping the Gunk

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

• Filter socks in a sump
• Filter floss or sponges in hang-on-back (HOB) filters
• Roller mats for higher-end systems

Swap or rinse mechanical media frequently—usually every 2–3 days—to prevent trapped debris from breaking down and fueling nitrates and phosphates. If you’re already running a sump, pairing your mechanical filtration with a protein skimmer is a powerful way to export organics before they decompose.

Biological Filtration: The Bacteria Engine

Biological filtration is the heart of your system. Beneficial bacteria convert toxic ammonia into nitrite and then into relatively safer nitrate. This happens on porous surfaces throughout the tank, including:

• Live rock and dry rock
• Bio media (ceramic rings, bio blocks, or spheres)
• Sand bed surfaces

A well-cycled tank with plenty of surface area can handle a surprising bioload, but it’s not instant. Always allow time for the nitrogen cycle to establish before adding sensitive fish or corals. If you’re unsure how to start, review our step-by-step guide on cycling a saltwater tank to avoid common mistakes.

Chemical Filtration: Fine-Tuning Water Quality

Chemical filtration uses media to remove dissolved substances that mechanical and biological filtration leave behind. Popular choices include:

• Activated carbon – polishes water, removes odors and toxins
• GFO (granular ferric oxide) – helps control phosphate and nuisance algae
• Resin blends – target specific contaminants (like organics or metals)

Run chemical media in a media bag inside a HOB filter or in a dedicated reactor for better contact time. Replace it on schedule; exhausted media can leach what it has absorbed back into the water.

Common Filter System Setups

There’s no single “right” filter system. The best choice depends on your tank size, budget, and livestock plans.

Hang-On-Back (HOB) Filters

HOB filters are great for nano and beginner tanks. They’re easy to install and maintain, and can hold mechanical, biological, and chemical media in one compact unit. To get the most from a HOB:

• Replace cartridges with reusable baskets and your own media (floss, carbon, bio media).
• Clean the impeller regularly to maintain flow.
• Pair with a small skimmer on larger or heavily stocked tanks.

Sump-Based Systems

Sumps are the gold standard for medium to large reef tanks. Water drains from the display into the sump, passes through filter socks or a roller mat, then a skimmer and media, before being pumped back up.

• Provides space for a larger protein skimmer and reactors.
• Hides equipment for a cleaner display.
• Allows for a refugium section with macroalgae for natural nutrient export.

Tip: Design your sump with easy access to filter socks or roller mats so you’ll actually keep up with maintenance. Convenience is a huge part of long-term success.

Canister Filters

Canister filters can work on saltwater systems, especially fish-only tanks, but they require diligent maintenance. They excel at mechanical and chemical filtration, yet can become “nitrate factories” if not cleaned regularly. If you use one:

• Rinse mechanical media weekly or biweekly.
• Avoid packing it with too much biological media if your rockwork already provides ample surface area.
• Monitor nitrates and phosphates closely.

Putting It All Together

An effective filter system is less about one magic device and more about a balanced approach: strong biological filtration, efficient mechanical removal of debris, and targeted chemical media when needed. Combine that with regular water changes and stable parameters—covered in detail in our saltwater aquarium maintenance guide—and you’ll have a clear, healthy tank that’s easier to care for and more enjoyable to watch.

Investing time into planning your filtration now saves you headaches later. Start with the system that fits your budget and space, keep it clean, and upgrade gradually as your reef grows.

Sources

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