How to Set Up and Cycle an Aquarium Filter with Seachem Matrix
By Pro Shrimp | Published: 2026-10-15
Category: How-to Guides
A step-by-step guide to setting up a filter and cycling your tank using Seachem Matrix, with practical checkpoints and common mistakes to avoid.
Quick answer
Set up your filter with mechanical media first, then fill the biological chamber with Seachem Matrix. Run the filter with a ammonia source and test daily until ammonia and nitrite read zero and nitrate appears. This usually takes two to six weeks. Keep the filter running and avoid overcleaning the Matrix.
Why Matrix belongs in the biological stage
Seachem Matrix is a porous inorganic solid about 10 mm in diameter. Each liter provides more than roughly 700 m2 of surface area, which supports both aerobic and anaerobic bacteria species. That makes it useful for controlling ammonia, nitrite, and nitrate. Place it after mechanical media so debris does not clog the pores. Rinse it in tank water before use; tap water rinse can harm the bacteria you are trying to grow.
Match the filter to your tank and flow
For nano tanks or aquascapes where an internal filter or sponge filter would be disturbing, an air-driven option like the Superfish Bio Air Disk can be hidden behind rocks, wood, or plants. It needs an air pump, which is not included. For canister or sump returns, the Hugo Return Pipe 13mm offers a durable stainless steel alternative to standard returns and is resistant to rust and corrosion in freshwater. It is not for saltwater aquariums. The dark interior helps prevent algae from clogging flow.
How much Matrix to use
Use enough Matrix to fill the biological chamber without restricting flow. A general starting point is 1 liter of Matrix per 100 liters of tank volume, but adjust based on your filter capacity and livestock load. If you cannot find a specific volume recommendation for your filter model, that is a decision limitation you will need to resolve by checking your filter manual or measuring the chamber.
Step-by-step filter setup and cycle
- Rinse and place mechanical media first: Rinse filter sponges or pads in tank water to remove dust. Put them in the first chamber so they catch debris before it reaches the Matrix. Checkpoint: mechanical media should be easy to remove for rinsing without disturbing the biological media.
- Add Seachem Matrix to the biological chamber: Fill the biological chamber with Matrix, leaving enough space for water to flow freely. Do not pack it so tightly that flow slows to a trickle. Common mistake: overfilling the chamber and reducing flow, which starves the bacteria of oxygen and waste.
- Start the filter and confirm flow: Turn on the pump or air pump and watch the return. Adjust the flow so it moves gently across the tank surface without blasting fish or plants. Checkpoint: if flow is weak, remove some Matrix or clean the mechanical media.
- Add an ammonia source to begin the cycle: Use a small amount of fish food or a pure ammonia product to raise ammonia to about 2-4 ppm. Do not add fish yet. Common mistake: adding too much ammonia at once, which can stall the cycle.
- Test daily and wait for zero ammonia and nitrite: Test ammonia, nitrite, and nitrate every day. When ammonia and nitrite both read zero and nitrate is rising, the cycle is complete. Checkpoint: this usually takes two to six weeks; do not rush it.
- Do a water change and add livestock slowly: Change 30-50% of the water to lower nitrate, then add a few hardy fish. Keep feeding light for the first week. Common mistake: adding too many fish at once, which causes an ammonia spike.
- Maintain the Matrix correctly: Rinse Matrix in tank water only when flow slows noticeably. Never rinse it under tap water or replace it all at once. Checkpoint: keep the filter running during maintenance to protect the bacteria.
Product facts
- Seachem Matrix: High porosity biomedia that provides efficient biofiltration for the removal of nitrogenous waste; controls ammonia, nitrite, and nitrate; supports aerobic and anaerobic bacteria species. This is the core biological media for your filter, so it handles the nitrogen cycle directly.
- Superfish Bio Air Disk: Airlift biological filter driven by an air stone; needs an air pump (not included). Easy to hide behind rocks, wood, or plants in small aquascapes or nano tanks. A good fit when a traditional internal or sponge filter would disturb your layout.
- Hugo Return Pipe 13mm: Stainless steel return pipe resistant to rust and corrosion in freshwater (not for saltwater); dark interior prevents algae from clogging flow. Useful for a sleek, durable return line on canister or sump setups without algae blocking flow.
