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How to build a 4'x4' Ebb & Flow Bioponics / Peeponics System

This document is step by step instructions on building and using a 4’x4’ ebb & flow bioponic system. All steps were taken to be as frugal as possible without compromising integrity or quality. Links are provided for convenience, I have no association with the vendors. Prices and links are sure to change.

Why use Bioponics over other methods?


If you are choosing soil-less methods for growing plants then you can choose to do either hydroponics, aquaponics, vermiponics, bioponics, or peeponics. I'm sure there are other methods but hopefully I covered most of them. Each has their pros and cons. This document will not cover each method since a person can easily obtain this information on the web. I will be focusing on bioponics/peeponics. 

Bioponics or Peeponics unlike hydroponics, allows you to use your own fertilizer (urine) so you never have to buy costly nutrients.The system is completely close-loop so it does not require flushing or draining of the nutrient tank. Unlike hydroponics, you aren't dumping nutrient effluent on to your soil, or down the drain possibly causing pollution to your soil and waterways. Another difference is in how we view bacteria. Hydroponics requires sterility, which is counter-intuitive to what occurs in nature. While with peeponics, we encourage good bacterial growth, working with nature to help grow our food.

Comparing it to aquaponics, you don't have to worry if the ammonia levels rise too high since plants can tolerate much greater amounts than fish. PH fluctuations and temperature changes will do less damage to your system as well. Additionally, not everyone wants to have, keep, or eat fish. After you are done for the season with your system, you don't have to worry about what you are going to do with your fish. I personally only care about growing plants and find learning how to keep fish happy an unnecessary chore. Pumps are less likely to clog as opposed to aquaponics. This makes solid waste filtration completely unnecessary. So overall we have more flexibility with PH, temperature, ammonia, nitrite, and nitrate levels without worrying about fish deaths.

If we look at how plants grow naturally in soil, we can see how this type of system mimics it almost precisely. Imagine a small patch of soil in a forest. A grazing deer urinates on this patch of ground before running off. The billions of beneficial bacteria living in-between each particle of soil converts the ammonia in the urine to nitrites and finally nitrates. A bird plucks some fruit from a tree and a seed drops on to the soil. A gust of wind blows some soil debris on top of the seed. The seeds starts its journey to becoming a plant. Each intermittent rain shower allows the roots access to more nutrients and when the soil dries, it allows oxygen molecules access to the root system. Worms eat decaying plant matter and move through the soil, leaving behind its own excrement in the tunnels it creates, allowing roots more nutrients and oxygen. More animals urinate and defecate nearby, more plants die and slowly rot, all adding nutrients via bacterial actions. There are intermittent rain showers and dry times, combined with plenty of sunshine. The plant thrives and matures...

This is exactly what we do in bioponics. We have our rain showers (ebb & flow), we have urine (human aged urine), and nitrifying bacteria,  and "soil" (coconut coir & perlite), and sun (light system or sunlight). We can even add composting worms to the system and they will thrive and benefit our system. Bioponics/Peeponics mimics this natural process, but with human intelligence and precision. We supply the nutrients in the amounts that are ideal, we control the PH, and we control the rain.

Why use Ebb & Flow over other growing methods?

I chose Ebb & Flow over NFT, Constant Flow, Aeroponics, Constant Drip, etc. for the reasons that I will explain below.
They are relatively easy to build and maintain, so complexity is kept to a minimum. The material cost is low for the amount of plants that can be grown. In case of any type of failure (ie pump, timer, power ,etc.) the system should be fine until a replacement part is found.  Since the bed need to be flooded only a few times a day (possibly less with certain media), very little electricity is consumed, very little noise, odor, and humidity is created. Very little evaporation occurs. In case of power failure, there is a two-tote system that can be implemented cheaply in order to "manually" work the system. There is no need for aerating the reservoir since the plants get plenty of O2 when the growing bed drains.

Since we use individual pots in this system, different sized plants can be grown in the same system and each plant can be moved around to suit the needs of the grower without disturbing the other plants. Root systems are very delicate so this is very important.

This system is also very well suited for indoor growing due to the above reasons (odor, noise,etc.) and that the shape is perfect for most light systems (no light movers are necessary).


Dispelling the Myths


Not enough nitrification - I tested my system that was only up for 2 weeks and it had almost no ammonia and lots of nitrates. Even though the media is only getting flooded every hour or so for only 15 minutes, it is more than enough time for a massive amount of nitrification to occur, especially if you've chosen your media properly. 

Timers more prone to fail - I found timers to be very reliable and fairly cheap. I have timers that have been working for years in the most horrid conditions.

Root rot more likely to occur - If you use a medium like coconut coir mixed with perlite you will have a great combination of moisture retention and drainage. This will discourage root rot caused by water-logged plants.


Items List

Qty. 1 - 4’ x 4’ Hydroponic Tray (ebb/flow aka flood/drain)

Function: You will be growing your plants in this "tray". It needs to be sturdy and hold 15 gallons of water, media, and plants without breaking, collapsing or buckling.

Cost: $59.00

This is the most important part of the system but can also be the most cost prohibitive. Shipping can be very costly for this type of item (due to size), it is better to buy locally if possible. if you can't afford or find a flood and drain table, you can use any shallow large plastic tub or container such as a Rubbermaid watering trough, or an IBC tote cut in half. You can even build your own with a modified table and a pond liner.

Size: This depends on how much space you have for this unit, how much you want to grow, and how much your nutrient tank can hold. I found a 4'x4' tray can hold roughly 60 5" net pots.


Qty. 1 - Ebb & Flow bulkhead fittings -

Function: These fittings will provide the way that your hydroponic tray will be flooded and drained with nutrient water.

Cost: $8.95


Qty. 1 - 22-30 gallon Plastic Tote w/ Lid

Function: Will be the nutrient tank, holding the water that will flood and drain your hydroponic tray.

Requirements: The three most important aspects to getting a tote is to make sure it is not clear/translucent (so algae doesn't grow in it) and that the dimensions of the tote allows it to fit under the “table” that will be holding the 4'x4' tray. Lastly you also want to make sure that the quantity of water it can hold is sufficient for your Hydroponic tray. A 4'x4' tray when filled (using just 1 overflow extension fitting) holds approximately 15 gallons.

Costs: $15

Qty. 1 - ½” black poly tubing

Function: This will be the tubing needed for your pump to push liquid to your hydroponic tray.

Required Amount: You will need a length of the distance between where your pump sits (at the bottom of your nutrient tank) and the bottom of your hydroponic tray, in my case, less than 3' (36")

Approximate Costs: $1.00

Qty. 12” - ¾” black poly tubing - You will need the the length of the distance between the bottom of your hydroponioc tray and  $1.59

Qty. 1 - Hydroponic Pump - - $27.55

You can get smaller pumps, but I recommend nothing less than 120 GPH.

Qty. 1 - Timer - - $10.99
Any timer that allows 15 minutes increments is sufficient. No need for digital or anything fancy.

Qty. 25 - (Preferably Square) 1 gallon nursery pots - These pots can be obtained sometimes for free. You can find nursery pots at any Plant Nursery. You can use any size you wish but the system is setup to be able to handle roughly 25 square pots (1 gallon size). You can also get (5" or 6”) net pots instead. If you can’t find any pots, then the cheap alternative is to rummage through other people’s recycling and find plastic 1 quart (yogurt) containers, milk bottles, etc. You will have to punch a few small holes in the bottom to allow for the wicking action. - $00.00

Qty. - 1 - 11 pounds of Coconut Coir - - $15.95

Qty. 1 Bag - Perlite

Alternatives to Coconut Coir mixed with Perlite can be vermiculite, sand, gravel, hydroton, rockwool, shredded wood bark, etc. I find that coconut and perlite provide the best air to water ratio, a ton of nitrification (critical for what we are doing) and cheaper and lighter than most media.

Costs: $12.48

Link: -

If you are having problems with bugs or vermin, you can use hydroton (aka clay pebbles) as media. It's a little costlier but easy to clean and reusable.

Qty. 1 - Stand/Table/Surface

Function: We basically need an item that can hold the 4'x4' tray. You can use your imagination for this item. You can use an old table, a desk, a bunch of plastic crates, or even put it on the ground (you would have to make sure the plastic tote is lower so gravity can feed the nutrient water back to the reservoir). I use 8 crates (2 stacked on each side) and it holds the tray fine.

Costs: $00.00

Total cost of all items - $152.51 (plus shipping,taxes, etc.)




Place the 4x4 tray on top of a flat level stand/table/surface. Making sure the plastic tote clears it underneath. I recommend having the tray no higher than 2-3 feet from the ground. The higher it is off the ground, the harder it will be for the pump to push the liquid from the reservoir to the tray.


Drill two holes (1 ⅜” in diameter) in the bottom towards one side of the tray (if they aren’t there already) these should be right next to each other (a couple inches apart). Make sure these holes line up to the tote as this is where the liquid will be pumped up and draining back down so measure properly where you want these holes to be. You want these holes at the lowest part of the tray, meaning where it is indented.


Place the tote (with the lid) exactly where you want it to be situated once the setup is ready. I recommend that the tote stick out a little bit from under the tray so that we can have easier access to it, in case we have to do any type of clean-up or refilling.


Insert a pen through the top of the holes that were drilled into the tray and have it make a mark on the tote lid. We are marking the holes that we will drill into the lid of the tote.


Drill two holes in the lid of the tote where you marked it in step 4. For simplicity, you can use the same 1 ⅜” drill bit for all the holes.


Attach the two bulkhead fittings to the tray, making sure the barbed ends are coming out the bottom. Hand tighten it as much as possible. You will not need most of the extensions, just make sure one of the fittings is slightly taller than the other. The taller one is the overflow drain (it will have a bigger diameter), while the shorter one will be used to pump liquid from the reservoir and it will also drain back down once the pump turns off.


Attach the ½” poly tubing to the pump, place it in the bottom of the tote and run the tubing up through one of the holes in the lid and connect it to the bulkhead that is shorter.


Attach the ¾” poly tubing to the other bulkhead allowing it to go through the other hole in the tote lid.


Fill the tote with water. Make sure to fill it nearly to the top (the pump should be off right now).


Plug in the pump and make sure it pumps up to the tray, fills the tray evenly. If it is pooling more to one side or another, you may need to re-level the stand. It is important that we get even distribution of liquid in all parts of the tray.


Leave the pump on for 15 minutes to watch for leaks and to make sure that the overflow drain is working properly. The timer will be set for 15 minute ON increments so we want to make sure that it fills completely during that period of time and that it is draining back to the reservoir.


Lift up the lid on the reservoir and make sure there is enough water above the top of the pump so the pump is not running dry. The more water we have on top of the pump, the better. We don’t want to have to refill the reservoir too often if we can help it.


Turn off the pump and make sure the water drains completely.


Media Preparation


Fill a 5 gallon bucket halfway with a piece of compressed coconut coir (use a flathead screwdriver and a hammer to chisel a piece from the block) and fill the bucket with water. Let it soak for an hour. Fill the rest with perlite. Use your hands and mix the perlite and coconut coir making sure to have a nice even 50/50 mix breaking up any large pieces of coconut, add more water as needed.


Fill up each pot with the mix until it reaches the top. Do not try to compress it.


Place each filled pot in the 4x4 tray until there is no more room left.


Set the timer for on every 1 hour for 15 minutes. Do not set it to go on at night. Make sure the plugs do not sit lower than the unit for safety reasons. Plug in the pump to the timer.


Cycling the system


 Add 1-2 cups of aged (3-4 week old) urine. Wait a few hours and check the ammonia levels. We want a level of about 5ppm. Keep adding, waiting and checking until this occurs. Once we have 5ppm of ammonia, make a note of how much urine you added. This will be the daily amount you want to add to the system (however this will change as your system matures or more plants are added). 


Allow the system to cycle for a week or two. Then check ammonia and nitrate levels. We are looking for ammonia levels to first go up (when you first added the urine), then go down as the ammonia is converted to nitrates. (Testing for nitrites isn't really necessary). Once the ammonia levels drop down to below 1-2ppm, we can add more urine. This process may take 1-3 weeks. Once we have a good amount of nitrates (>20 ppm), it means the nitrification cycle is working properly and we can start adding plants or seeds.


Maintenance and upkeep

The main thing to watch every week (or more frequently in hot weather) is the level of the water in the reservoir, make sure to top it off as needed. We don’t ever want the pump to run dry, it will greatly reduce the life of the pump, possibly destroying the pump. Unlike hydroponics, we never need to dump and replace the nutrient water since we are not adding salts that will build up in the system. Although a once per season flush with regular water is not a bad idea just to clean out rotted roots, dead bugs, and other debris.

Check nitrate levels daily at first, if they fall below acceptable levels, add more urine. You may be able to do this weekly once you establish a pattern based on observation and recording your results.

PH checks should be done weekly as well. As long as the PH is within 5.9-7.0 we are okay. The nitrification process tends to be an acidic one, so you may need to buffer the PH by filling an empty pot with crushed oyster shell (easily obtained at amazon) or crushed egg shells and placing it in the tray. This will buffer the ph with every flow.

Every week, clean up the bulkhead fittings to prevent plant matter from clogging the fittings.

Every month, check and clean the pump to make sure that it is not getting clogged. Since there is nothing but water and urine going through the pump, you won’t have many issues with clogged pumps.

Harvest and trim plants as needed.

Check for bugs weekly. Bugs can easily be controlled using a fine mist sprayer mixed with a little bit of soap and water. Make sure not to miss the underside of the leaves as that is where a lot of bugs hide. Do not bother with diatomaceous earth since it only works in dry environments and will not work properly with an ebb & flow system.

Optional Indoor Setup


Hang a 400 watt Metal Halide/HPS (aka Sodium Vapor) Lamp from the ceiling using chains (at least 2-3 feet from the tallest plants so they don’t get burned). You can also use Fluorescents if you are growing only greens/low-light veggies although you may not be saving money on power consumption by doing so.


Have the lights turn on 16 hours and off 8 hours. You can set another timer to do this.


Do not spray anything while the Lights are on. If the MH/SV lamps gets wet, they can explode.


You may need a small fan to remove the heat from the lamp as well as to help the plants stem’s get stronger from the breeze.


 Updated: 12/15/2014 (two years after initial article, I've learned a lot, and included those lessons in the update)

Views: 9809


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Comment by Vlad Jovanovic on November 21, 2012 at 11:23am

Meir, your a man after my own heart! 

I'll be testing out/experimenting/playing-around-with-while-making-observations some more this winter with the 'all humonia derived' 3-part bio-hydro nutrients I've been making with that whole "humonia/struvite' thing in the hopes of mitigating some of the issues pee-ponics presents in relation to fruit bearing cultivars. My hope is to not need any P or K additions that are not derived from humonia. If you think a biological phosphate recovery (and by extension potassium) process could aid you in your endevours...I'd be happy to help. Free of charge of coarse ...

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