Refugium Setup Guide: How to Grow Chaeto for Nutrient Export

A refugium is a separate, connected chamber (or external tank) in a reef aquarium system where macroalgae like Chaetomorpha (chaeto) grows under dedicated lighting to remove nitrate and phosphate from the water column. A properly sized refugium running Chaetomorpha can reduce nitrate by 10–20 ppm per week in a 100-gallon reef system — without the need for chemical filtration media or water changes alone.

Why Refugiums Work

Macroalgae like Chaetomorpha absorbs nitrate (NO₃) and phosphate (PO₄) as nutrients for growth. When you harvest and remove the algae from the refugium, you permanently export those nutrients from the system — a process called nutrient export. Unlike a protein skimmer (which removes organics before they become nitrate), a refugium removes nitrate and phosphate that have already formed, making the two complementary rather than competing.

Refugiums also serve as refuge zones for copepods and amphipods — beneficial microfauna that supplement the diet of mandarin dragonets, wrasses, and other planktivorous fish.

Refugium Sizing

A refugium should be 10–20% of the display tank volume for meaningful nutrient export. For a 100-gallon reef tank, a 10–20 gallon refugium compartment provides sufficient space for a dense chaeto ball that can be harvested weekly. Larger refugiums (25–30% of display volume) provide more stable pH buffering through the photosynthesis/respiration cycle.

Refugium Light Requirements

Chaetomorpha grows best under red (630–660nm) and blue (430–470nm) wavelengths. LED refugium lights designed specifically for macroalgae cultivation — like the Seatorch MC-95, which outputs a 6500K spectrum with enhanced red channels — produce faster chaeto growth than generic full-spectrum LEDs. Run refugium lights on a reverse photoperiod (lights on when display lights are off) to stabilize pH: as chaeto photosynthesizes overnight, it consumes CO₂ and raises pH, counteracting the natural pH drop during darkness.

Chaeto Growth and Harvesting

Healthy chaeto doubles in mass approximately every 2–4 weeks under good lighting and nutrient availability. Harvest 25–50% of the chaeto ball weekly, leaving the remainder to continue growing. Remove harvested chaeto from the system — do not let it die in the tank, as it will release stored nutrients back into the water.

Inline vs External Refugiums

Type	Setup	Best For	Cost
Inline (sump compartment)	Built into sump	Most reef systems	Low (existing sump)
External hang-on	Clips to display tank	Sumps without refugium section	Medium ($80–$300)
External plumbed	Separate tank, plumbed in	Large systems, dedicated macro culture	High ($300–$800+)

FAQ

Can I use a refugium instead of a protein skimmer?

They serve different purposes. A skimmer removes organics before they become nitrate; a refugium removes nitrate and phosphate after they form. Using both is standard practice in well-maintained reef systems.

What is the best macroalgae for a refugium?

Chaetomorpha (chaeto) is the most popular: it grows fast, doesn't go sexual and crash like caulerpa, and is easy to harvest. Gracilaria (ogo) is also effective and provides supplemental food for tangs.

How long does it take a refugium to lower nitrates?

Expect 2–4 weeks before seeing measurable nitrate reduction in a new refugium. Once chaeto is established and growing vigorously, weekly harvesting typically removes 5–20 ppm nitrate per harvest in a 100-gallon system.

Do I need to dose CO₂ in my refugium?

No. Unlike planted freshwater tanks, refugiums don't require CO₂ supplementation. Macroalgae growth is limited primarily by nutrients (nitrate, phosphate) and light, not carbon availability.

How do I know if my refugium light is strong enough?

Healthy chaeto should visibly grow within 2 weeks. If chaeto turns pale or fails to expand, increase photoperiod first (target 12–18 hours), then consider a higher-output refugium light.