ACTIVITY: Aquaponics in a Bottle

NGSS Science and Engineering Practices
NGSS Crosscutting Concepts

The activity below draws from the content in the page Ecosystem Cycling.



Image caption

Fig 1. Parrotfish help cycle matter by expelling fine-grain coral sand on a tropical reef at Palmyra Atoll. Palmyra Atoll is in the center of the Pacific ocean basin.

Image copyright and source

Image by Ingrid Knapp

Animals take in matter when they eat and lose matter when they poop (Fig. 1).


How does matter cycle through the ecosystem?

Guiding Questions:

  1. Where do plants get the energy they need to survive?
  2. Where do animals get the energy they need to survive?
  3. What happens to the food that animals eat?


Create your own mini aquaponics system in a bottle and observe the relationships between organisms. 

Note: Hydroponics is the method of growing plants in water (without soil). In comparison, Aquaponics is a system that combines aquaculture (the growing of aquatic animals, like fish, snails, clams, etc.) in combination with hydroponically grown plants.

If you haven't already played the aquatic food chains game, check it out on the bottom of this page: Ecosystem Cycling!

Note to teachers:

This aquaponics-in-a-bottle activity is a simple model using a recycled 2L bottle. You can can adapt the activity to build a larger or more complex aquaponics system. To connect the hydroponics activity to this aquaponics one, click the activity extension below, which will guide you through procedures to set up an alternative system in a two-part series. You will first establish a hydroponic system in a larger tank. You will then add fish to the system to create a more complete and cycling ecosystem.

Materials (per aquaponics bottle):

  • Student worksheet and teacher guide (attached below):
    This teacher guide follows the procedure written here and in the student worksheet with additional instructions and guidelines. We highly recommend starting this activity by introducing the Phenomenon, Inquiry, and Guiding Questions from the top of this webpage.
  • One clear, two-liter plastic bottle (soda, juice, or iced tea containers work well)
  • Extra container to hold water for water changes
  • Serrated bread knife and cutting board, or scissors
  • Aquarium gravel, or small rocks (enough for about 2 inches at the bottom of your bottle)
  • Drill with small drill bit (or alternative tool sharp enough to poke a hole in the bottle cap for plant roots to go through)
  • Water
  • One aquatic organism: One small fish (a snail and/or shrimp may also be used)
  • Fish food (can be purchased from a pet store)
  • Small starter plant or a cutting that has been "rooted" (herbs like basil grow easily and work well)
  • Optional: Two skewers for holding the top of the bottle in place
  • Optional: Aquarium aerator, with tubing and airstone. (You can purchase splitters so multiple tubes with airstones can be divvied to separate aquaria.)
  • If possible, take students on a field trip to collect organisms, like small fishes and snails, from nearby streams. You will need one small fish per bottle. If you cannot collect enough organisms for the entire class, you can purchase small fish from a pet store. 
  • Allow the water to sit out for at least 24 hours so the chlorine in the tap water evaporates (or use commercially available drops to treat the water).
  • Do not put the bottle aquarium in direct sunlight as it will overheat the water and increase algal growth. 
  • If the top portion of the bottle doesn’t sit at the right height, you can use wooden skewers as support beams. Poke two holes all the way through the top portion of the bottle and place wooden skewers through them. Allow them to protrude about an inch on each side. These will allow the planted section to sit higher above the aquarium.
  • Aquaponics is an excellent way for students to explore their use of engineering principles. Encourage your students to modify the design in this activity based on the materials they have access to! If possible, allow students to iteratively modify their aquaponics set-up for optimum plant growth and fish health. 

Important Note to the Teacher:

Invasive species concerns: It is important to dispose of organisms (plants, fish, snails, etc) properly so that native habitats are not harmed. If appropriate, you can return organisms to the place where you caught them, but do not release organisms bought from the pet store into the natural environment. The release of pet store guppies is likely the reason for their presence in Hawaiian streams and their negative impact on native species: https://dlnr.hawaii.gov/ais/other-ais/guppies/.

Please see http://www.habitattitude.net/ for guidance on aquarium disposal.

Care of living organisms: This activity involves observation and experimentation with small fish, which are vertebrates. Consideration of proper, humane care of vertebrates is important.  Provide explicit guidance for students to develop an understanding of and value for life and living organisms. The fish must be provided with appropriate daily care so that they remain healthy during the course of the experiment and should not be subjected to pain or discomfort.

Students need to be supervised by a teacher that understands the safe and responsible use of animals in the classroom and who understands and follows Hawai‘i Department of Education policies and other relevant regulations. Teachers must develop and implement a plan for the future care of the fish and other organisms following the study.

(Adapted from the National Science Teacher Association’s 2005 Position Paper: “Responsible Use of Live Animals and Dissection in the Science Classroom”)

Proper care of small fish, like guppies includes:

  1. Feeding them daily, i.e. making sure there is a source of food such providing fish food.
  2. The temperature of the water must be between 72° and 82° F.,
  3. Change approximately 1/3 of the water every 1 to 2 weeks, or as needed to keep the water in good condition.
  4. Create a happy or natural environment by adding things like gravel and plants to the tank. Care of the fish must be provided daily, including weekends, holidays, and other times school is not in session. When the experiment is over you must continue care of the guppies in the classroom or implement another plan for the continued proper care of the guppies, as they cannot be re-introduced into Hawai‘i’s environment. 

If students take their aquaponics-in-a-bottle home: Make sure that students and their families are aware of the type of organisms that are coming home, their required care (do they need to take home fish food to keep the fish healthy?), and the proper disposal procedures (can they go back to a local stream, or are they from a pet store and need to be treated differently?).

For further information regarding current policies and regulations in Hawai‘i: Contact the Science Section of the Instructional Services Branch of the Office of Curriculum, Instruction, and Student Support at the Hawai‘i Department of Education.

The above recommendations may be downloaded in this activity sheet.


  1. Follow along on your worksheet to build an aquaponics system in a bottle!
  2. Before you begin, answer these questions:
    1. How do scientists study plants and animals in their natural habitats?
    2. What might be some limitations, challenges, or risks with studies in the natural environment?
    3. What is the ethical treatment of living things? How will you ensure your animals are being treated ethically?
    4. Why do animals, including humans, eat things?
    5. Do plants eat?
    6. What is a producer? Consumer? Decomposer?

*NOTE* The procedural steps call for letting your water sit, rocks soak, and rinsed plant roots soak for 24 hours. You can do all these steps at the same time before you start constructing the aquaponics-in-a-bottle.

Build your aquarium:

  1. Prepare your water by allowing it to sit in a container exposed to the air for 24 hours. This will allow the chlorine to evaporate. (Chlorine is used to keep tap water from becoming contaminated with algae or bacteria). You can also use commercial drops to treat your water before using it in your aquaponics system.
  2. Rinse your aquarium gravel and allow it to sit in water for 24 hours to remove any toxins.
  3. Rinse and scrub the two-liter bottle with clear water to get rid of any residue inside and to remove any labels from the outside. Do not use soap!
  4. Cut off the bottle top at the shoulder (where the bottle tapers).
    Note: Cut the bottle so the lower aquarium portion will have a bit of curvature at the top (Fig. 2). 
    Image caption

    Fig. 2. A serrated bread knife works well for cutting large plastic bottles. Cut your bottle at the so the lower aquarium portion will have a bit of curvature at the top.

    Image copyright and source

    Image by Kanesa Duncan Seraphin

  5. Add a layer of small aquarium rocks to cover the bottom two inches. Rocks are important for two reasons:
    1. Rocks keep the water clearer by holding fish poop and uneaten food particles, which keeps them from floating in the water.
    2. Rocks provide a surface for good bacteria to live on. These bacteria help to convert the fish waste into nutrients that are usable by plants.
  6. Fill the bottle with prepared water. Leaving about an inch and a half of space at the top.

Get your plant zone ready: 

Image caption

Fig. 3. A small drill bit was used to make a hole in the top of the bottle cap.

Image copyright and source

Image by Kanesa Duncan Seraphin

  1. Use a drill to make a hole in the bottle cap (Fig. 3). The hole should be big enough to pull the plant roots through, but small enough that the plant stem will not slide through.
  2. Prepare your plant roots to pull through the hole in the bottle cap.
    1. Rinse the roots. This is especially important if you are using a plant that was started in dirt.
    2. We recommend soaking your plant roots in clean water for 24 hours.

  3. Pull your plant roots gently through the hole in the bottle cap (Fig. 4a and 4b). 

    1. Some of the roots will break off. That is okay!


Image caption

Fig. 4a. A basil plant and roots before pulling the roots through the hole in bottle cap.

Image copyright and source

Image by Kanesa Duncan Seraphin

Image caption

Fig. 4b. Basil plant with roots pulled through the hole in the bottle cap.

Image copyright and source

Image by Kanesa Duncan Seraphin

  1. Set your plant zone on top of your aquarium, or a another water source, while you continue to set up your aquaponics-in-a-bottle. 
    Image caption

    Fig. 5. This style of bottle does not have ridges. Skewers are used to hold the top portion in place.

    Image copyright and source

    Image by Emily Sesno

  2. If the bottle top doesn't rest on the brim of your aquarium, you can use wooden skewers as support beams (Fig. 5).
    1. With help from a teacher, poke two holes on opposite sides of the bottle top and slide wooden skewers through them. Allow them to protrude about an inch on each side. Do this on both sides. Rest it on top of the bottle aquarium. 

Add your fish: 

  1. Make sure your water has been sitting out and rocks and roots have soaked in clean water for 24 hours.
  2. Add your fish to the aquarium! 
    Image caption

    Fig. 6. Complete aquaponics-in-a-bottle with aquarium rocks, a small fish, and a basil plant.

    Image copyright and source

    Image by Kanesa Duncan Seraphin

  3. You may add another small creature, like a snail, that you think would be a good fit for the ecosystem.
    1. Keep in mind this is a very small aquarium, so don't add very much. One small fish and one snail are a good amount!
  4. You may add an aquarium decoration if you like (but make sure it is non toxic and has been rested in clean water for 24 hours).
  5. If you have an aerator, position your aquarium near a plug and plug in the aerator. Place the airstone in the aquarium.
  6. Put the plant side on top of the aquarium.
  7. Make sure the water level is correct.
    1. Your plant roots should be in the water, but there should not be standing water inside the plant dome. 
    2. Add or pour out water as needed to get the right level.
  8. Your aquaponics-in-a-bottle is now complete (Fig. 6)!

Care for your ecosystem!

Note: In nature, the cycling of matter between producers, consumers, and decomposers allow the ecosystem to thrive without external input. However, since this system is small and will likely not represent all aspects of a natural ecosystem, you will still need to feed the fish and water the plant to ensure they are getting enough energy.

  1. FEEDING: Drop a few flakes or pellets (depending on food choice) on the surface of the water to feed the fish few days (every 2 or 3 days should be fine).
  2. CLEANING: You will need to replace about 1/3 of the water every 1-2 weeks as needed. This will prevent algae buildup and ensure enough oxygen is available (The plants will contribute to the oxygen available).
    1. Prepare replacement water the day before, allowing it to sit out for 24 hours to evaporate any chlorine.
    2. Remove the top and scoop out about 1/3 of the water using a cup (a soup ladel works well). Be careful not to scoop the fish with the water!
    3. If there is algae build up on the exposed walls, you can wipe it off with a paper towel or clean sponge to prevent overgrowth.
    4. Pour in fresh water slowly so as not to stir up any loose particles.
  3. Make observations of your system over time and answer the questions on your worksheet. 
  4. Engineer changes to your system! Aquaponics systems benefit from regular attention and tinkering. Do not be afraid to change things in your system as time goes on!

Activity Questions:

  1. Match the vocabulary words with their definitions below. Then use the information to answer the activity questions.


    1. An organism requiring food, which it gets by eating other organisms.
    1. An organism, often bacteria, fungus, or invertebrate, that breaks down waste from other organisms.
    1. Organisms that use energy from the sun and matter in air and water to grow.  
    Primary Producer  
    1. Any substance that has mass and takes up space by having volume.
  2. What role does your plant play in making food from matter your ecosystem-in-a-bottle?
  3. What role does your fish/snail play in moving matter your ecosystem?
  4. What role does the bacteria living on the rocks play in recycling matter in your ecosystem?
  5. Which organism in your ecosystem is a:
    1. Primary producer?
    2. Consumer?
    3. Decomposer?
  6. How do the organisms in your ecosystem work together to recycle matter and produce food?
  7. Draw your own food web based on your ecosystem in a bottle (there are many correct food webs!). Label the primary producer, consumer, and decomposer. 
  8. What might happen if a higher level predator was introduced to your ecosystem (such as a crayfish, large fish, or large frog)?
  9. Is there evidence of any other plant life in the aquarium? (Hint: It is possible that microscopic freshwater algae may have grown, and if it becomes dense enough may appear either as a greenish film, or perhaps a greenish hue in the water.)
  10. How are models beneficial to scientists when studying plants and animals?
  11. How could you improve your design for a future aquaponics system?

Related Conversations


The plastic bottle version of this activity is super user-friendly, but it also uses plastic. So, I tried to create a glass and fabric version. I used an old olive jar and a mesh shopping bag. I grew sprouts through the mesh shopping bag. This worked well (although I recommend trimming the fabric so that it will not wick away the water out of the jar!), but is more dangerous because of the glass. It is also more expensive and temperamental because of the fabric. However, I am confident that students can engineer some creative solutions!

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I experimented with using air stones and a bubbler that I bought at the local store because I was concerned with keeping my fish alive. It turned out that I did not need the bubbler, but it might be needed if the ecosystem is overcrowded—especially if you use aquatic plants inside the bottle, which photosynthesize during the day (supplying oxygen to the system) but not at night (when their biomass continues to respire and may consume so much oxygen that the fish cannot survive).

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Exploring Our Fluid Earth, a product of the Curriculum Research & Development Group (CRDG), College of Education. University of Hawai?i, 2011. This document may be freely reproduced and distributed for non-profit educational purposes.