Cleaner fish are one of aquaponics’ best-kept secrets — introducing the right species into your system creates a natural biological maintenance crew that controls algae, consumes waste, and reduces your workload without any chemicals or manual effort.
What Are Cleaner Fish in Aquaponics?
Cleaner fish is a term borrowed from marine biology, where certain fish species perform cleaning services for larger fish by eating parasites, dead skin, and debris. In aquaponics, the concept applies to smaller fish or invertebrate species that perform maintenance functions within the system — eating algae, consuming uneaten food, processing waste, and in some cases controlling pest organisms.
These species work alongside your primary fish (barramundi, silver perch, etc.) and contribute to a more self-managing, biologically diverse system.
Popular Cleaner Species for Aquaponics
Bristlenose Catfish (Ancistrus spp.)
Bristlenose catfish are among the most effective algae cleaners available for freshwater aquaponics. They rasp algae directly from tank walls, pipework, and grow bed infrastructure with their sucker-style mouths. They’re peaceful, hardy, breed readily in appropriate conditions, and coexist well with most aquaponics fish species. A small population of 3–6 bristlenose in a standard backyard system provides excellent ongoing algae management. Temperature preference: 22–27°C.
Common Catfish (Hypostomus plecostomus)
The common pleco is a larger relative of the bristlenose and provides similar algae-cleaning services. They can grow quite large (30–50 cm), which limits their suitability in smaller systems. Hardy and long-lived, they’re best suited to larger systems where their size is an asset rather than a management challenge.
Siamese Algae Eater (Crossocheilus oblongus)
An excellent algae grazer that actively consumes various algae types including the challenging black beard algae that most other species ignore. Active swimmers that patrol the entire tank. Best kept in groups of 3+. Temperature preference: 24–26°C.
Goldfish
Goldfish are the classic beginner’s aquaponics cleaner fish. They consume algae, uneaten food, and organic debris, are extraordinarily hardy, and are available everywhere. While they don’t provide a table fish harvest, they’re excellent for ornamental or beginner systems where fish management simplicity is a priority. They can also serve as the primary fish in a system while you learn aquaponics management before committing to more demanding species.
Freshwater Shrimp (Neocaridina and Caridina spp.)
While technically crustaceans rather than fish, freshwater shrimp are superb cleaners in aquaponics systems. They consume algae, biofilm, decaying plant matter, and organic debris continuously. Their small size means they’re at risk of being eaten by larger fish — keep them in separate compartments or in systems with only small, peaceful fish. Cherry shrimp (Neocaridina davidi) are the most widely available and adaptable species.
Crayfish
Freshwater crayfish are efficient waste processors and can be a primary harvest species in their own right. They consume organic debris, algae, and dead matter. The main consideration is their tendency to be opportunistic — they may catch and eat slow or sick fish if the opportunity arises. Best housed separately or with fast-moving fish. Check state regulations on crayfish species — some native species are protected.
How to Introduce Cleaner Species Successfully
- Research compatibility — Ensure your cleaner species can coexist with your primary fish in terms of temperature, pH, and behaviour
- Introduce gradually — Add cleaner species to your cycled, established system; quarantine new additions before introduction
- Maintain appropriate numbers — Too many cleaner fish increases the overall bioload; start conservatively and monitor system parameters
- Provide refuges — Pipes, rocks, and hiding spots reduce competition stress and give smaller cleaners refuge from larger fish
Frequently Asked Questions
Will cleaner fish compete with my main fish for food?
Most cleaner species eat algae, biofilm, and organic matter rather than competing directly for commercial fish feed. Some, like goldfish, are omnivores and may consume some pellets — but in practice the competition is minimal in a well-managed system with appropriate feeding quantities.
Can I keep bristlenose catfish with barramundi?
Yes, in most cases. Bristlenose are small (usually under 15 cm), bottom-dwelling, and peaceful. They occupy a different niche to barramundi and coexist well as long as the barramundi aren’t large enough to consume them as prey (juvenile barra may attempt to eat very small bristlenose). Introduce bristlenose when they’ve reached 5+ cm to reduce predation risk.
Do cleaner fish need separate feeding?
In most established aquaponics systems, cleaner species find sufficient food in algae, biofilm, and organic matter without supplemental feeding. If algae levels are very low (a sign of a healthy, well-managed system), offer occasional algae wafers or blanched vegetables like zucchini to supplement their diet.
Will shrimp survive in a system with larger fish?
It depends on the fish species and size. Many larger fish will eat shrimp given the opportunity. Shrimp are best maintained in separate grow bed compartments, in tank sections with plant or pipe refuges, or in systems with only small, peaceful fish. Dense plant cover in the grow bed can provide enough refuge for shrimp populations to sustain themselves even with some predation.
What’s the best cleaner fish for controlling algae on tank walls?
Bristlenose catfish are the top choice for tank wall algae control in freshwater aquaponics systems. They’re specifically adapted to grasp and rasp algae from hard surfaces, are hardy across a wide range of conditions, and are widely available from aquarium suppliers across Australia.
Want to build a naturally self-managing aquaponics system? Get the complete build guide here and start your thriving ecosystem in just 2 hours.