AP Manual


Aquaponics is a sustainable method of farming that uses both hydroponics (growing without soil) and aquaculture (raising fish).  Water from the fish pond is intermittently pumped into gravel filled grow beds containing plants.  Bacteria living in the gravel, compost the fish waste into fertilizer for the plants.  Plants absorb the fertilize, and the cleaned water slowly drains back into the pond to be recycled.  



The pond contains a pump connected to a timer, an aerator, and sometimes a heater (depending on your selection of fish).  The grow beds are water tight boxes containing nitrifying bacteria, gravel, and planted vegetation.  Both the pond and grow beds are connected through a series of pipes to help circulate and recycle the water.


How System Works

Fish living in the ponds are fed regularly in their comfortable aerated aquatic environment.  A set timer attached to the submersible pond pump, periodically passes water into the grow beds.  When the water comes into contact with the nitrifying bacteria rich gravel inside the grow bed, it is both mechanically and biologically filtered.  The byproduct of this filtration process is captured solids and fertilizer.  Plants and microorganisms then absorbs the byproduct and fresh cleaned water is drained back into the pond to provide a comfortable environment for the fish.  



Usually attached close to the electrical outlet and connected to the pump, the timer should be set for 1 hour on and 1.5 hours off.  1st cycle begins 1 hour after sunrise and ends 1 hour before sunset.  Timer should be completely off during the night.  Check weekly to make sure timer is accurate.



This is a pump located outside in a shady area with a tube that drops into the bottom of the pond.  Attached to the end of the tube is a diffuser that creates oxygen for fish and bacteria to breathe.  The aerator stays on 24 hours a day.  Aerators last around a year before needing to be rebuilt.  Make sure to always have rebuild kits on standby in case your aerator goes out.


Pond Pump

Attached to the timer, the pump is responsible for transporting the water into the grow beds.  
Pump should be removed weekly from the pond and checked to make sure the impeller is spinning properly and free of debris.  



Usually made of PVC and ABS, plumbing connections should be checked for leaks every 3 months.  If clogging occurs, 1st try pressurizing the lines by shutting off ball valves attached to pump and top of beds.  If pressurizing is unsuccessful, a snake can be used to clear out there lines.  There is also usually a clean-out fitting for maintenance.  



Valve attached closes to pump is called the relief valve.  The relief is responsible for dispersing pressure between the pond and the lines going into your beds.  Tighten the relief, beds get more water pressure, open relief and pond gets more pressure.
Valves located on top of beds are used to regulate pressure going into bed.  When multiple beds are attached to one pump, bed valves can be used to distribute flow evenly to each bed.    


Pre Filter

Before water enters into bed, it passes through a pre filter to prevent solids from the water to enter into gravel.  Pre filters should be cleaned out every couple days.



Located in the grow beds, there are usually 2 types of gravel.  Bottom quarter of bed is 2” gravel so water can pass through freely, while the top three quarters is 3/8” gravel for plants and bacteria.  It is very important that gravel is cleared of all roots and debris before starting a new plant.  Use a three prong hand cultivator after plant has been harvested to rake and remove all debris in the area.  Flooding the bed before and during cleaning makes this process much easier.  You should be able to run your fingers through the gravel when cleaned properly.  Root bound clogged gravel will cause anoxic problematic environments and flooding in bed, be sure to clean regularly.      


Drain Pipe

Located on the far end of the bed, opposite to the fill valve and housed with some sort of cover to protect gravel from spilling in; the drain pipe keeps water from over flowing and help beds drain after being filled.  Pipe is connected to a bulkhead through hole fitting and can easily be removed for maintenance.  Make sure pipe is always pushed in completely to prevent bed overflowing.  There are 2 holes on the fill pipe that allow the water to drain once the bed is finished filling.  These 2 holes and the pipe housing should be scrubbed with a pipe cleaner weekly to prevent and clogging in the system.


Adding Water

Water should be added to the system directly into the pond weekly.  Typical water loss is about 10% per month in the summer, and about 0-5% in the winter (depending on your location).  When adding, be mindful of the chlorine that may be present in city water as it may cause damage to your fish and bacteria.  You can add water on a continuous drip into the pond so chlorine levels never reach a dangerous amount, or fill quickly with a solvent like sodium thiosulfate that will dissolve the chlorine from the water when added.  


Feeding Fish

Each different specie of fish has specific dietary requirements that you should be familiar with when choosing your feed.  Throw small amounts of food into the water until the fish stop eating.  If 5 minutes has gone by and the fish are still not eating, they are done.  Remember this amount for the next feeding and repeat.  As fish grow they will eat more.  Use the 5 minute method to determine how much to give them.  Excess food can dirty water and cause ammonia spikes in the system.  Be careful not to overfeed fish.  Fish can be fed up to 3 times per day.  


Sowing Seeds

After area has been thoroughly cleaned and the bed is completely flooded, level out all the gravel so it is 1 half inch higher then the water line.  Drops seeds in desired area about 3 inches apart and gently massage them into the gravel so they drop to the waterline.  Be sure to set timer back to normal and not to add too many seed as it will make thinning them out later very difficult.  



Always to be done in the evening or on cool overcast days not to lose the plant to shock, first step is to flood the bed.  Once bed is flooded, scoop 3 to 4 inches beneath desired plant and lift out the plant, roots, and connected gravel.  Dig a small similar shaped hole in another desired location and place plant in gently.  Make sure this area is also flooded with water.  


Supplemental Fertilization

Once you have identified what nutrients are needed in your system, prepare the mixture in a pre mixed bucket diluted with at least 5 gallons of water.  Make sure all the water in the system is drained out of beds and back into pond.  Add mixture of nutrients to pond and turn pump on immediately so water can be circulated.  Never add amount of nutrients that can be toxic to fish, plants, or bacteria.  It is recommended you do small batches per week to not shock the system. 

AP Next Steps


    Now that your farm is built, here is a guide to help you get your system up and running!  Each phase is listed in chronological order from first to last steps to system maturity.  An aquaponic system is essentially an accelerated microcosm of our planets preexisting natural balanced ecosystems.  Each of these steps are essential in order for your farm to create the optimum environment for successful production.    



Now that the system is built, the next thing we need to do is build up your beneficial bacteria.  The bacteria are responsible for creating a safe environment for both the fish and plants to live together, and it is very important we start here. This process is called cycling, cause we are going to cycle nutrients throughout the pond and beds to inoculate and propagate bacteria growth.  Once a system is cycled, you should never have to repeat the process.  Your farm should be running (ebbing and flowing) 24 hours a day for this process, that way the nutrients can constantly cycle throughout the entire system.  It is also very important your aerator is plugged in.  The bacteria your cultivating are aerobic and require DO (dissolved oxygen) to thrive.  This aerator is also very important for your (soon to come) fish and plants to be healthy as well.  

To start, turn off your system so water isn’t pumping out, and drain all the water from your beds back into the pond.  Once all the water is out of the beds and into the pond, make sure your pond is filled to your desired (full) amount.  We don’t want to add any water during the cycling process, so its best to top off your pond now.  

Now that your pond is topped off (full), add your ammonium nitrate to the water until you measure 5ppm ammonia.  The best way to do this is to add a very small (measured) amount, stir water, and then test within 5 minutes.  I usually add about ¼ cup per 2000 gallons.  The potency of your ammonium may differ, so just start slow and increase as needed.  Once you’ve tested your water, determine the amount you’ll need to bring your system up to the desired 5ppm.  If you added too much, don’t stress, you can always do a small water change to dilute the ammonia.  Once you’ve figured out your dosage, write it down - you’re going to add the exact amount multiple times throughout the cycling process.   Now turn your system back on and let the ammonia cycle throughout the beds and pond.  Pond timer should be a constant 1 hour on and 1.5 hours off to achieve the desired ebb and flow.  

Every 3 days, test the water.  You should see the ammonia begin to drop, this means the bacteria is beginning to grow in your beds!  Measures the amount the ammonia dropped down, and add more to bring it back to the 5ppm.  

In about 2/3 weeks, you should begin to see nitrite in your system.  Nitrite is a by-product of the ammonia-consuming bacteria in your system.  You are now 1/3rd of the way through your cycling process.  Since your ammonia is now being converted to nitrite, it will be difficult to measure how much you need to add.  Refer to your recorded log of the 2 weeks prior and repeat the regimented dosage amounts.  

In about 4/6 weeks from the start of the cycling process, you will then begin to notice your ammonia is undetectable because it is being consumed immediately by bacteria.  You will also notice that your nitrite levels are beginning to decrease and your nitrate levels are increasing.  Congratulations, you are 2/3rds of the way through the process.  If you have plants in your system, you will be unable to detect the nitrate because it is being consumed by the plants, so instead just watch for the nitrite to decrease.  Continue your dosage.

In about 6/8 weeks, your ammonia and nitrite should be undetectable.  This means your bacteria is present in the grow beds and doing its job.  In order to test your bacteria efficiency, turn system off and drain beds (like we did in the beginning), and add 5ppm ammonia to the pond, then turn system back on.  In 24 hours, test for both ammonia and nitrite – if both are undetectable, you’re ready for fish!

The entire cycling process should take 6/8 weeks.  Since bacteria thrive in warmer environments, you can add heat to water to speed up cycling process.  

Here is a chart to show how the nitrogen levels fluctuate during cycling  



Add Water

Now that your system is cycled, its time to refill your pond.  Turn off pump, drain beds, and get all the water back into the pond.  Before filling pond, make sure you de-chlorinate the water.  Now that we have live bacteria in our system, it is very important we don’t add anything that can harm them.  For now on, every time we add water to our farm, we always de-chlor, no matter what.  Chlorine is harmful for not only the bacteria, but the fish and plants as well.  Also, you should be adding a little water regularly rather then a lot irregularly.  This will be way less stressful for your fish, and reduce the chances of harming your bacteria because it will have such a small impact on the total volume of pond.  

To de-chlor, it is best to treat water before it enters the pond – this way your fish will never come in contact with chlorine.  Whatever solution you use to de-chlor, the bottle will give you the recommended dosage on the side.  

If you are unable to treat water before it enters into pond, add both water and de-chlor simultaneously.  Rather then throwing a hose in the pond and then dumping solution in after, first determine how much water your going to be adding.  Do this by finding out the fill space in cubic feet in your pond, and then multiplying that by 7.48.  This will give you how many gallons you’re going to be adding.  

Example:  if your pond is 4’ deep, 4’ long, and 4’ wide, and you have 1’ of fill space to your desired amount, multiply Length (4) x Width (4) x fill space (1).  This will give you 16 cubic feet.  Now multiply 16 x 7.48 (gallons in a cubic foot).  This is 119.68 gallons.  

Now you know exactly how much solution you need to add.  Take the dosage and divide it by 4.  Add the first dosage before you add any water, then begin to fill with hose.  Once you hit the 1st quarter mark in pond, add second dosage, and so on.  This way your removing chlorine molecule in pond before it has time to react with fish.


Set up Ebb and Flow

You no longer need water to cycle 24 hours a day, but instead we want to create an optimum environment for the plants that are in your grow beds.  Your going to keep the same ebb and flow time of 1 hour on and 1.5 hours off , this is more then enough retention time for your ammonia to react with the bacteria in your beds.  Set the timer to begin an hour after sunrise, and end an hour before sunset.  You will have to adjust your timer periodically as the days get shorter and longer, and we have time changes.


Add Fish

When adding fish, make sure you allow them to slowly acclimate into their new environment.
If fish come in bag – place bag in pond and let it float on surface for 15/30 minutes.  Make sure the water temperature in the bag is equal to temperature in pond.  Once temperatures are equal, slowly poor fish from bag into pond. 
If fish are in cooler or tub – Gradually remove water and add small amounts of pond water over the course of 30 minutes.  Once both tub and pond share the same temperature, slowly pour fish into pond.
Make sure both the bag and tub are heavily oxygenated during the acclimation process – fish can only survive so long without dissolved oxygen – might be a good idea to throw an air stone in bag or tub.  



After the construction of the system and once the water is flowing, plants can be added at anytime.  You can burry seeds 1 inch deep in the beds, or transplant seedlings directly into the media.  If you are transplanting, make sure you do it in the evening so the sun doesn’t dry out your plant while its getting used to its new environment.  Plants added before or during cycling will not have the adequate nutrients they desire, so be sure to add a small amount of organic liquid fertilizer to the pond to help feed your plants.