Aquaponics Basics: How Fish, Plants, and Microbes Work Together
Aquaponics is a food production method that combines recirculating aquaculture, or fish farming, with hydroponic plant production. Fish release waste nutrients into the water, microorganisms convert those wastes into plant-available forms, and plants remove nutrients as they grow. When properly designed and managed, aquaponics allows water and nutrients to be reused within the system.
Integrated fish and plant production has historical roots dating back to rice-fish culture in ancient China and Mesoamerican chinampas where crops were grown on floating islands in lakes. Modern aquaponics builds on these ideas by combining recirculating aquaculture with hydroponic plant production and using filtration, aeration, and microbial activity to convert fish waste into plant-available nutrients.
This publication is intended for homeowners, educators, growers, Extension professionals, and community organizations interested in understanding the basic principles, benefits, limitations, and components of aquaponic systems.
Key takeaways
- Aquaponics combines fish, plants, and microorganisms in a recirculating system.
- Fish waste provides nutrients, but solids removal and biofiltration are essential.
- Ammonia and nitrite can harm fish if water quality is not managed.
- Aquaponics can conserve water but requires reliable power, aeration, and monitoring.
- System success depends on balancing fish health, plant growth, and microbial activity.
Is aquaponics right for you?
Why aquaponics matters in Arizona
Arizona’s hot, dry climate and limited water resources make water-efficient food production systems especially important. Aquaponics can reduce water use by recirculating water through fish and plant production systems. However, Arizona conditions also create challenges, including high summer temperatures, evaporation, energy costs, and the need to maintain adequate dissolved oxygen for fish and beneficial microorganisms. Successful aquaponics systems in Arizona require careful attention to system design, shade, cooling, aeration, water quality, and fish and crop selection. Many of these considerations also apply to other arid and semi-arid regions where water conservation, heat management, and reliable aeration are important.
How do aquaponic systems work?
The three living components of aquaponics
An aquaponics system depends on the interaction between:
- Fish or aquatic animals that generate waste nutrients
- Microorganisms that convert waste into plant-available nutrients
- Plants that remove nutrients from the water.
Maintaining balance between these components is essential for long-term system stability and productivity
Water quality management
- Temperature: Affects fish health, plant growth, and microbial activity
- Dissolved oxygen: Needed by fish and nitrifying bacteria
- pH: Affects nutrient availability and ammonia toxicity
- Ammonia: Toxic nitrogen form that should not accumulate
- Nitrite: Toxic nitrogen form that should not accumulate
- Nitrate: Plant nutrient and indicator of nitrification
Nitrification
Nitrification involves the conversion of ammonia (released by fish) into nitrate. Nitrate is much less toxic to fish than ammonia or nitrite at typical aquaponic concentrations and is the major form of nitrogen used by plants. Ammonia is converted to nitrate by naturally occurring bacteria in the presence of oxygen that colonize surface area within the aquaponics system. Therefore, adequate surface area is required to eliminate all the ammonia produced by the fish each day, and this is done in a biofilter. A variety of media types can be used to provide surface area for the bacteria, including sand, gravel, plastic beads, and other small plastic media specially designed for biofilters. Each type has benefits and drawbacks.
Simplified nitrification process in aquaponics. Beneficial microorganisms convert ammonia from fish waste into nitrite and then nitrate, a plant-available form of nitrogen.
Graphic by Matthew Recsetar using AI-assisted image generation.
System design and components
Although aquaponics systems vary in design, most systems contain several core components that maintain water quality and recycle nutrients. Because fish and beneficial microorganisms require oxygen, most aquaponics systems rely heavily on aeration and water circulation. Oxygen is critical to fish, biofilters, and mineralization and can be delivered via air pumps and air diffusers.
Types of aquaponic systems
- Media bed systems: Plants are grown in gravel or expanded clay media that also acts as biofiltration.
- Floating raft systems: Plants float on rafts above nutrient-rich water (also known as deep water culture systems).
- NFT systems: Nutrient film technique systems use a thin film of water that continuously flows through channels containing plant roots.
Core components of an aquaponics system
Core components include fish tanks, solid filtration, biofiltration, plant growing area, pumps and plumbing, aeration, and monitoring equipment.
Basic components of a recirculating aquaponics system. Water flows from the fish tank through solids removal and biofiltration before reaching the plant growing area. Water then collects in a sump and is pumped back to the fish tank.
Graphic by Matthew Recsetar using AI-assisted image generation.
System filtration and solids digestion
Solids removal
Uneaten feed and fish feces produce suspended and settleable solids that can reduce water quality if they accumulate. Solids should be removed before they break down further in the system. Many aquaponics systems draw water from or near the bottom of the fish tank so heavier solids can be carried to a clarifier or mechanical filter.
Solid removal methods include:
- Radial flow clarifiers
- Swirl filters
- Sedimentation basins
- Bead filters
- Microscreen filters
Biofiltration
Adequate surface area is required to eliminate the ammonia produced by fish, which is housed inside a biofilter.
Common biofilters include:
- Moving bed biological reactors (MBBRs)
- Trickling filters
- Upflow biofilters
- Downflow biofilters
Solid digestion (mineralization)
Solids removed from the aquaculture system can be further broken down through aerobic digestion, also called mineralization. This process can release nutrients that were trapped in solid waste and may produce stabilized biosolids that can be used in some agricultural or garden applications, depending on local regulations and food safety considerations.
Getting started with aquaponics
Before building a system
Consider the following questions before building or purchasing a system:
- What is the purpose of the system? (education, hobby, research, or commercial production)
- Do you have available space, electricity, water source, and drainage?
- Do you know which fish species you will choose and their temperature requirements?
- Which plant species will you grow?
- Will this be to sell or for household use?
- What size system do you want and what will that cost?
- Do you need monitoring equipment for your system?
- Do you have backup aeration or emergency planning for power outages?
Basic startup steps
- Define the purpose of the system.
- Select fish and crops that match the local climate and system goals.
- Draw a system plan and estimate water flows, tank volume, filtration needs, and electrical requirements.
- Purchase components and assemble the system.
- Fill, circulate, and aerate the system.
- Establish biofiltration before fully stocking fish.
- Add fish gradually while monitoring ammonia, nitrite, nitrate, pH, dissolved oxygen, and temperature.
- Add plants and continue monitoring system performance.
- Harvest and make adjustments as needed.
Common aquaponic plant production methods. From left to right: media bed system, floating raft system, and NFT system.
Matthew Recsetar