How to Start Your Aquaponic System

How To Start Your Aquaponics System

Get growing quickly by following these simple instructions.  Regardless of whether you are starting a small or large aquaponic system, we have designed the following information to apply to any scenario so that you get the best results.  Follow these steps after you have set up your system.

Step 1.  Add Grow Media

Add grow media into the growbed(s).  We highly recommend that you use 3/4″ river rock.  This not only is an inexpensive solution, but you will get the extra added benefit of introducing worms into your system (their eggs are just naturally in the rocks).  Fill the growbed so that there is 12″ of grow media in the growbed.  (NOTE:  Do not fill higher than 12″ because this will increase changes for anaerobic bacteria to build up which will kill plants, microbes and fish.)  Make sure the media is evenly distributed, level and does not cover the water spout that brings water to the growbed.

Step 2.  Add Water

Fill up your fish tank (and sumps) with water.  If you are using a tap water, you will need to turn on your pump and aerator to bubble off chemicals that are commonly found in municipal waters.  It usually takes 3 days (for small systems) to 1 week (for large systems) to completely get these chemicals out of the water. Keep in mind that you will need to aerate the water when you need to add more water to your system to plant uptake or evaporation.  Chlorine hurt fish and plants.  There are ways to expedite this process.  Simply use a chlorine remover to treat the water.  Add 5 ml per 50 US-gallons of tap water to remove chloramine.

Step 3. Add Plants

Now that you have the right PH, the next step is to add plants into the growbeds.  You can add plants into the system even though your water may not be clean.  (They will help clean the water and absorb healthy nutrients.)  If you are adding plants grown in soil, it is imperative that you get as much of the soil off the roots as possible.  As a best practice, we recommend using vermiculate as a growing medium to start plants in.  This growing media easily rinses off and eliminates the potential of cross contamination of e-coli or other harmful bacterias or pathogens into your aquaponic system.

To plant plants, simply dig down into the grow media 2″ and gently place the plant and roots into the grow media.  Carefully return the grow media being sure to not damage the roots or cover the leaves of the plant.  Make sure that the plant is supported and standing upright.  As you add plants, make sure to provide enough space between them so they have room to grow.

It is natural for plants to go into shock after they have underwent a transplanting process.  What will typically happen is that the outer leaves may wilt or die.  Monitor plant health for the next week.  You should see the new growth start to grow which will indicate that they are establishing themselves in the system.  If the plant is not recovering, check to make sure that the plants roots have been planted deep enough to reach the nutrient-rich water.  If the roots are not deep enough, reposition the plant and continue to monitor for improvements.

Step 4. Test the PH

Using a PH test kit, test the water.  When the range is between 6.5 to 7.5, it is time to add fish (proceed to step 4).

Step 5.  Activate the Nitrogen and Nitrate Cycle

In order to prepare your aquaponic system to support fish, we need to establish the healthy microbes and bacteria that will convert their ammonia waste products into “bite size” chunks for the plants to absorb.  To do this, you will need to add ammonia into your water.  Use the following to determine how much ammonia to put into your system:

  • Small (1 to 100 gallons)– Start with one cup.  Add one capful everyday for 2 weeks.
  • Medium (101 – 500 gallons) – Start with a pint.   Add one capful everyday for 2 weeks.
  • Large (500 plus gallons) – Start with 16 ounces/500ml on day one and every day after only add 1oz/30ml for 2 weeks

Every day to every other day testing the ammonia, nitrite, and nitrate levels to see the cycle move through.  Once you see this happen were no ammonia shows and little to no nitrites as well.  It is safe to add fish to the system.  This can take 2 weeks.

Another way to add the beneficial bacteria to your system is by using MicroBacter.  Simply, add two teaspoons for every 10 gallons of water.  Then test your water quality to measure PH, ammonia, nitrates and nitrates every other day in the beginning and then once a week thereafter.

Left to right, pH, Nitrite, Nitrate, Ammonia

Left to right, pH, Nitrite, Nitrate, Ammonia

Step 6.  Add Fish

Now that your aquaponic system has clean water with the right PH and has healthy microbes to deal with ammonia and fish waste, the next step is to add fish.  There are many different types of freshwater fish that will work in these systems.  In order to determine what the best fish for you and your system is, we encourage you to Contact Us.  Once you decide and have purchased your fish, add them into your fish tank.


  1. If you establish a fish colony with bacterial for a couple weeks…do you need to use the ammonia? Cant you establish the bacteria naturally with put the chemical?

    1. the bacteria need a food source and that is what the ammonia provides. If you start with fish, they make the ammonia but there is a period where there isn’t any bacteria so you run a risk of the fish dieing and to avoid this you might need to change the water to get rid of the excess ammonia until there is enough bacteria to do this job.

    2. if you have fish already, chances are you already have the right bacteria. the wrong bacteria puts out a bad odor so what is one way to tell if you start cultivating the anaerobic bacteria. Fish produce ammonia so don’t add it if you have fish.