Setting up Aquaponics Systems

LESSON 1: Media Bed Technique

Introduction

There are three common aquaponic techniques that we have briefly discussed in the
previous module. We will look into each of them a little further so that we can distinguish the
most apt technique when you will be constructing your own.

The media bed technique is the most popular design, especially for small-scale aquaponics.
Usually, it is used when one wants to experiment or try out aquaponics – and decide
whether to expand the farm as a business or for commercial use.

In general, using media-filled bed units are ideal for beginners because of space
efficiency, low cost, and simplicity. With the media bed technique, the medium supports
the roots of the plants. And this same medium becomes the biofilter and the mechanical
filter – making it cost-efficient and simpler, without needing supplementary equipment and
pieces of machinery.

However, the media bed technique can be disadvantageous because of their limited fish
stocking ability where the media may be clogged – ending up with needing more filters.
Furthermore, there is high water evaporation since media beds are exposed to the sun.

There are also aquaponic designs that combine other techniques. These lessons merely
serve as standard and do not strictly enforce that techniques should be done solo or as is.
There are various designs that combine depending on available resources and techniques
in recirculating aquaponics

Take note however that there are also variations of media bed techniques aside from what
you will learn in this lesson.
TOPIC 1: Water Flow Dynamics

Source: Small-scale aquaponic food production, FAO

One of the main distinguishing features of differentiating an aquaponic technique to another

is by understanding how the water flows through the system.

In the media bed technique, the water flows through gravity from a filter into the media bed.
The media beds are made up of porous biofilter media which serve as a biofilter and
mechanical filter. The media beds will be the place where the nitrification process occurs
as well as where the plants will grow. After the water flows through the media beds, the
water goes down to the sump tank through gravity. It is then free of solid and dissolved
wastes becoming clean water. Then, it is pumped back again to the fish tank until it
overflows and returns to the media bed—completing the cycle.

In this method, the oxygen is complemented through the process and given to the plant
roots and aids in the biofiltration of ammonia.
TOPIC 2: Media Bed Construction

Media bed aquaponics in TESDA Green Technology Center

In creating the media bed, one must choose its materials first. Ideally, it would be made
from plastic containers, but you have the option of fiberglass or wooden
frame (supplemented by water-tight rubber or polyethylene sheeting on base and inside of
walls).

 The Do-It-Yourself version would be made from plastic containers, modified IBCs, or any

unused household equipment that can hold the system as long as it is strong enough to
hold water without breaking, weather-proof, safe for the biological components, and can be
easily connected with other units.

The ideal shape would be a rectangle of 1 meter in width by 1-3 meters in length. One can
easily scale to create larger beds as long as there would be additional support since the
water capacity may make the bed collapse. It should also be well-sized enough so that the
aquaponic farmer would be able to handle its components easily.

The depth of the media bed is around the size of 15 – 30 cm depending on what is grown.
Larger vegetables would require 30 cm while leafy vegetables would require around 20 cm.
TOPIC 3: Choice of Medium
The medium or the growing media will need to have enough surface area since water and
air needs to permeate through it for the plant to get all the nutrients it needs. 

In general, the growing media should be inert, non-toxic, neutral pH, and not dusty. The
media is usually washed before being placed into beds because it might be too airy. It will
need to be compressed before being used as a medium. Any medium that the aquaponic
farmer can use as long as it meets the standards can be used. It should be lightweight,
cost-efficient, and has good drainage.

The following are common growing media used in aquaponics:

1.    Volcanic gravel

Photo from https://aquaponictrend.blogspot.com/2018/11/lava-rock-aquaponics.html

This is one of the most widely used media in media bed units and most recommended. It
has a very high surface area to volume ratio, cheap, easily obtainable as long as it is
available in the area, and inert. It is also available in many locations. Furthermore, it is
recommended that the size would be 8 – 20 mm in diameter since smaller sizes of gravel
may clog the solid wastes.

2.    Limestone
It is used but not recommended because of its low surface area to volume ratio. Since it is
a sedimentary rock, it is also heavy and may not be inert. As a sedimentary rock, it is prone
to dissolve in water and may affect water quality, increasing the pH of water. It is only
allowable to use in cases where the water is naturally acidic so that there would be a
counterbalance so it would act as a buffer for the water.

3.    Light Expanded Clay Aggregate (LECA)

This is also called LECA for short. It consists of expanded clay pebbles. Widely used in
hydroponics, they are light, round-shaped pebbles. They are more expensive compared to
other media. Its size would be similar to volcanic gravel and can even be incorporated in the
insulation of rooftops where the aquaponic may be placed by using LECA.
TOPIC 3: Choice of Medium
Common grow media

TOPIC 3: Choice of Medium

Different growing media
Check out this table from FAO to see the comparison of different growing media as well as
the alternatives one may use in case the common media are not available.

Media Type Surface pH Cost Weight Lifespan Water Plant Ease to

Area Retention Support Work
(m2/m3) With
Volcanic 300-400 Neutral Medium Medium Long Medium- Excellent Medium
gravel (tuff) Poor
 Volcanic 200-300 Neutral Medium- Light Long Medium Medium- Easy
gravel High Poor
(pumice)
Limestone 150-200 Basic Low Heavy Long Poor Excellent Difficult
gravel
Expanded 250-300 Neutral High Light Long Medium- Medium Easy
clay (LECA) Poor
Plastic bottle 50-100 Inert Low Light Long Poor Poor Easy
caps
Coconut fiber 200-400 Neutral Low- Light Short High Excellent Easy
Medium

TOPIC 4: Filtration

As previously mentioned, media beds are most efficient with filters both biofilter and
mechanical filter. The media bed technique makes use of a combination filter and plant
growing area where the mineralization process occurs as well.

The media bed as a mechanical filter acts as a physical filter that captures and contains
solid and fish waste and organic debris. This will depend however on the medium used that
is why in the previous topic, the diameters are noted because more packed medium will be
able to capture more.

Furthermore, media beds can be clogged with solid when other factors such as feed rate
are unbalanced. In case of the failure of the media bed as a mechanical filter, the medium
will need to be rewashed – disturbing the process of plant growth and nitrification, slowing
down the whole process.
The media bed as biofilter shows how the growing media that have large surface areas
are ideally where the nitrification occurs. This can be lost however when the media bed
becomes anoxic (meaning that oxygen is depleted). This happened when water quality is
bad or if temperatures drop.

Mineralization in the media bed occurs naturally. But in the case where mineralization is
not enough – manifested through sludging in the media bed because the breaking down of
fish waste and other materials into nutrients are not enough, one must provide a separate
filtration system to filter the waste separately aside from the media.

TOPIC 5: Media Bed Zones

It is important to understand that in a flood-and-drain media bed, it has three separate
zones that are also micro-ecosystems. These are separate smaller ecosystems because of
their different water and oxygen content. In each zone, a group of bacteria, fungi,
microorganisms, worms, insects, and crustaceans are present. Other species also act in
breaking down fish wastes.

This topic provides a brief overview of how the three zones as ecosystems act.

1.    Dry Zone
The top 2-5 cm space of the bed. It acts as a light barrier to prevent fungal growth and harmful
bacteria at the base of the pp stem. This zone also reduces evaporation by covering the wet area
from direct sunlight.

2.    Dry/Wet Zone

The top 10-20cm space where the media bed floods and drains from time to time. This zone has
moisture and has a high gas exchange. The biological processes occur in this zone where the root
development, good bacteria, and good microorganisms are all active. Because of the presence of
air and water in this area, all the animals/bacteria and plants gain the benefits.

3.    Wet Zone

The bottom 3-5 cm space of the bed. This zone is always wet. It has small solid waste
accumulations that is why most of the organisms that are responsible for mineralization are
found in this zone. This is where waste is broken down into smaller particles to be absorbed by
the plants.

TOPIC 6: Media Bed Irrigation

Different irrigation techniques are utilized depending on the system or if the system needs
adjustments. It is also important to note that the aquaponic farmers’ experience with the
different technologies should be accounted for in operating different dynamics of irrigation.

The most widely used method in the media bed technique is flood-and-drain or ebb-and-
flow. This is where the system floods the media bed with water from the fish tank then
draining it back to the sump tank. This can be done through autosiphons or timed
pumping.

Water cannot be always present in the roots because the plants and bacteria will also need
adequate airflow for the roots to be able to breathe. Through this process, moisture is
retained and oxygen levels are replenished.

1.    Bell Siphon
Photo from https://worldwaterreserve.com/aquaponics/bell-siphon-for-aquaponics/

This method is an autosiphon technique that was also shown in the previous topic. In a bell
siphon, the media bed is flooded and drained automatically from time to time without a
timer. But this technique will require the attention of the farmer since it is dependent on the
water flow to the bed.

The water flows slowly and constantly in the bell siphon. The water drips from the standpipe
as the grow bed is filled. The bell part of the bell siphon creates a constant water height
environment and locks as the water continues to fall – thus the siphoning effect.

A bell siphon consists of three components:

(1) Standpipe – a PVC pipe, 2.5cm in diameter and a height of 22 cm (for standard media
bed sizes). It passes through the bottom of the bed connected to the sump and the water
path in draining.

(2) Bell – a PVC pipe, 7.5cm in diameter and a height of 25 cm. A PVC end-cap is placed
on top. It has an open bottom where it is fitted on the standpipe. It has two rectangular gaps
(1x4cm) at the bottom of the bell and 1.5 cm up on opposite sides where water is pulled to
standpipe instead of a bell. A 1 cm hole is drilled 5 cm from bottom to break siphon.
(3) Media Guard – a PVC pipe, 11 cm in diameter and a height of 32 cm. It has many holes
drilled in the sides. This prevents gravel from grow bed clogging and entering the standpipe
while not blocking the water flow.

2.   Timer Mechanism

This method uses a timer switch on the water pump to have periodic flooding and draining.
This has no autosiphon and may be easier for beginners. There is however lesser filtration
because of little water circulation and aeration. This is not recommended when having high
tank stocking.

References
Somerville, Christopher. Small-Scale Aquaponic Food Production: Integrated Fish and Plant
Farming. Food and Agriculture Organization of the United Nations, 2015

LESSON 2: Nutrient Film Technique

Introduction

Nutrient Film Technique, or simply NFT, is a method used in hydroponics where horizontal or

vertical pipes with a shallow stream of nutrient-infused aquaponic water pass through. The
plants are placed on holes on top of the pipes.

This technique, along with DWC to be discussed in the next lesson, is popular in commercial
production because they are efficient in larger scales. However, they will cost more when
starting up compared to media beds.

TOPIC 1: Water Flow Dynamics

The water in NFT flows through gravity from the fish tank. The water passes through
the mechanical filter then into the biofilter and sump tank. Water is then pumped in two
directions through a valve. Some of the water returns to the fish tank while the other pumps into
a system where water is equally distributed through the NFT pipes.

After the water flows through the tanks, it returns to the biofilter and sump tank where it is
pumped again in the same way. The fish tank will overflow when water enters thus returning the
excess water to the mechanical filter.
LESSON 3: Deep Water Culture Technique

Introduction

Deep Water Culture, or simply DWC, is an aquaponic technique where the plants are
suspended on polystyrene sheets while their roots are hanging down to absorb the
aquaponic water.

 This technique, like NFT, is usually used in commercial aquaponics. In DWC, usually, one
high-value crop is planted for mass food production. Usually, the crop would be lettuce,
salad leaves, basil, and others. Take note that this is complicated to set up and maintain
when it is done in small-scale aquaponics.

 The polystyrene sheets have several holes drilled where net cups or sponge cubes (acting
similarly like grow media, but in this method, the net cups, for example, are filled with the
grow media to further support the seedlings) are placed to support each plant. Smaller
plants can be distanced closely while larger plants may require some distance across each
other.

 In this lesson, we will go through how the water flows in the system as well as the filter
system and canals used for DWC.
TOPIC 1: Water Flow Dynamics
DWC and NFT are largely similar in many aspects. This includes how the water flows by
gravity through the filter and to the biofilter, all from the fish tank. In the biofilter/sump tank,
the water is pumped through “Y” valves, distributing the water in two.

Some of the water goes back to the fish tank, while the rest of the water is distributed
through the canals. From the grow canals (where the plants are located), the water flows
again and exits on the other side and returns to the biofilter/sump tank. From the
biofilter/sump tank, it is pumped again into the fish tank or to the canals. The water entering
the fish tank will cause the tank to overflow and exit again into the filter – repeating the
whole cycle.

Photo from FAO

TOPIC 2: Filtration
Filtration in DWC and NFT techniques are identical.

To review: In this system, it will need separate filters constructed. A mechanical which will
be able to gather all the solid wastes and a biofilter where the nitrification process may
happen.

There are different designs for the filters, some may even be high-end and complex. An
example would be a mechanical swirl filter that will gather wastes where a screen acts as a
filter to trap any solids as it travels to the biofilter.

The biofilter is usually lined with air stones and has separate biofiltration media where the
nitrification process can occur.
TOPIC 3: Grow Canals
The length of grow canals may vary from 1 to 10 meters. Just like in NFT, as long as there
are adequate water inflow and re-oxygenation that reach all the plants, plants can grow
optimally and obtain nutrients.

Canals can be made of any strong static materials that can hold water. These materials can
be the same materials used in building fish tanks. These can be fabricated IBC plastic
containers, fiberglass, wood, concrete blocks (as long as it is lined with waterproof seals
and sheets), and other sturdy materials.

On another hand, narrower and longer canals will provide a quicker water speed. This will
benefit the roots by having better nutrient flow and absorption.

The ideal depth of the canals is 30 cm for the roots to thrive efficiently.

Photo from https://www.epicgardening.com/deep-water-culture-get-started/

TOPIC 4: Aeration
Aeration is very important in DWC units. If there are many crops planted in the system, this
means that there is a higher demand for oxygen because the oxygen levels will fall below
the minimum if the plants do not have an adequate amount.
The most recommended aeration method would be having air stones. These can release 4
liters of air per minute. They are placed equally, having 2 - 4 m 2 of space in the canal.

An alternative would be using venturi siphons. They are inserted on the water inflow pipes
which will aerate the water as it enters the canal
 Venturi siphon (DIY, T-style)

Another would be using the Kratky method. In this method, a space of 3 – 4 cm is left in

the space between the water and the polystyrene sheet. The air will be able to circulate on
the top section of the plant roots and provide adequate oxygen to the roots. This is ideal in
many cases as it prevents direct contact of the water to the plant stems, preventing various
diseases, and in tropical areas will favor heat dispersion from the water.

Kratky Method, Photo from FAO

References
“Cylinder Air Stone, Large 4″.” Go Green Aquaponics,
gogreenaquaponics.com/products/cylinder-air-stone-large-4.

Affnan's Aquaponics. “Aeration - Trying to Get the Most from Siphon Outlet - Part 2.” Aeration
- Trying to Get the Most from Siphon Outlet - Part 2, 26 Aug. 2010,
www.affnanaquaponics.com/2010/08/aeration-trying-to-get-most-from-siphon_26.html.

Somerville, Christopher. Small-Scale Aquaponic Food Production: Integrated Fish and Plant

Farming. Food and Agriculture Organization of the United Nations, 2015.

LESSON 4: Assessing the Ideal Aquaponic Technique to Use

Introduction

Now that we have learned the different aquaponic techniques that are being used all across
aquaponic farms, we are going to look into what technique is best for your needs. If you
want to start your aquaponics farm, it is better to start with simple media bed techniques
since this is the only method for small-scale aquaponics for now. It is also cheap and
relatively easier to set-up compared to NFT and DWC techniques.

In this module, we are going to guide you in building your small scale aquaponic system.
But it is important to understand the various aquaponic techniques especially if we plan to
expand the farms and produce commercially. Whereas in NFT and DWC will save you a lot
of money in bulk food production compared to the media bed technique.

For this lesson, we are looking at the strengths and weaknesses of the three techniques
discussed in this unit. We will also look at how aquaponics can be a modern solution to food
insecurity as well as how it is currently practiced in the Philippines.

TOPIC 1: Strengths and Weaknesses of the Media Bed Strengths and

Weaknesses
TOPIC 2: Strengths and Weaknesses of NFT
TOPIC 3: Strengths and Weaknesses of DWC
TOPIC 4: Prioritizing Food Production

Aquaponics may be a fairly new food production practice but it already has provided many
benefits over simple aquaculture or hydroponic system alone. Having a shared system
creates a sustainable, efficient system – saving cost, energy, water consumption, etc.
However, aquaponics requires the basic knowledge of how the units are engineered and
may need the training to train aquaponic farm workers too. But in the long run, with a larger
system and lesser cost, aquaponics can be the solution to food insecurity in many
countries.

References
Shahafi, Maryam, and Daniel Woolston. “Aquaponics: A Sustainable Food Production System.”
ASME, IMECE2014-39441, 2014.

Somerville, Christopher. Small-Scale Aquaponic Food Production: Integrated Fish and Plant

Farming. Food and Agriculture Organization of the United Nations, 2015.
UNIT 2: Explaining the Biological Components of Aquaponics Systems

LESSON 1: Explaining the Role of Bacteria in Aquaponics

Introduction
Bacteria are ‘microscopic, single-celled organisms that thrive in diverse environments’
(Livescience).

They are organisms which can live almost anywhere – soil, water, and even inside the
human body. 

Bacteria are organisms essential in the whole aquaponics ecosystem. Without bacteria, fish
waste will not be converted into plant fertilizer. Since we have already learned about the
nitrogen cycle as well as the biofilter, we are going to review and at the same time, look
further into the various bacterial goods that work in aquaponics.

Additionally, heterotrophic bacteria is introduced and discussed. We will learn about how it
performs mineralization of fish waste. We will also look into unwanted bacteria such as
denitrifying bacteria, sulphate-reducing bacteria, and pathogens.

TOPIC 1: Role of Nitrifying Bacteria

The nitrifying bacteria is responsible in converting fish waste. First, as ammonia, then into
nitrate which is fertilizer for plants.

Nitrification is easily described in two steps: 

First, nitrifying bacteria convert ammonia to nitrite through ammonia-oxidizing bacteria or

AOB.

AOB are bacteria from the common group Nitrosomonas.

Secondly, nitrite is converted to nitrate by nitrite-oxidizing bacteria or NOB.

NOB are bacteria from the common group Nitrobacter.

Note that nitrifying bacteria are slow to reproduce and create colonies. It might take weeks
to establish the bacterial colony in the aquaponic system. It is important to add little fish in
the system at first as too much fish may cause the system to fail because bacteria may not
be able to fully adapt and function at the start.

Remember that the reason we do not use a transparent, glass fish tank is because bacteria
will need a large and unlit area to colonize with water, food, and oxygen.
TOPIC 2: Role of Heterotrophic Bacteria

While we have understood that nitrifying bacteria are responsible in converting the
ammonia, that’s where heterotrophic bacteria come in. It metabolizes the organic
byproducts through the process of mineralization – creating essential micronutrients for the
plants.

Source: Small-scale aquaponic food production, FAO

Mineralization is done by releasing the nutrients found in the solid waste into the
water. Since plants cannot absorb the nutrients of the solid organic byproducts, it will need
to be broken for the roots to be able to absorb these. 

Mineralization highly aids in answering issues of nutrient deficiency and fertilizer needs of

plants. At the same time, the heterotrophic bacteria also feed on the organic matter
available in the aquaponic system. 
Heterotrophic bacteria are found where the solid wastes accumulate. It also has similar
living conditions with nitrifying bacteria except that heterotrophic bacteria reproduces in
hours compared to weeks.

TOPIC 3: Preventing Unwanted Bacteria

In general, there are three kinds of unwanted bacteria commonly found in an aquaponic
system.

Denitrifying bacteria

These anaerobic-thriving bacteria are responsible for the process of denitrification – where
nitrate is converted back into atmospheric nitrogen, becoming unusable for plants.
Denitrifying bacteria are commonly found along with the other bacteria however, such
bacteria will reduce efficiency in the aquaponic system by removing natural fertilizers.

Sulphate reducing bacteria

This group of bacteria, like denitrifying bacteria, thrive in anaeraobic (oxygen-less)

conditions. They obtain energy through a redox reaction with sulphur, however this process
creates hydrogen sulphide (H2S) that is highly toxic to fish.

 
Pathogenic bacteria 

These bacteria may bring diseases in plants, fish, and even humans. These bacteria may
be harmful and will need to be treated separately. By following good agriculture practices,
such harmful diseases may be avoided in aquaponic systems. This also applies to using
proper PPEs, good hygiene, good quality fish feeds and good water quality management,
and preventing pests such as rodents that may bring diseases.