5 Causes of Clogging in Hydroponics (and Solutions)

Pipes and hoses are standard components of most hydroponic systems. But, clogging of these tubes is a major detriment to gardeners who only want a sweet harvest of their labor. Luckily, I’ve developed hacks to prevent and solve clogging in my hydroponic system over the course of my experience.

In general, clogging in hydroponics is a result of algae bloom, overgrown roots, loose growing mediums, suspended solids, and small tube diameters. All of these can be addressed by maintaining optimal temperature, preventing light from reaching the water, trimming the roots, establishing strong roots before transplanting, and using filtered water.

As we move forward, I will reveal key secrets that I use in my hydroponic garden. Since I began doing these, I have always had a bounteous harvest at the end of every growing cycle. And I am telling you, you are not going out of this article without them.

1. Algae Bloom

Algae populations can dominate the nutrient water and clog hydroponic pipes. They can also reduce the amount of nutrients in the hydroponic solution and compete with the plant.

For us to perform efficient ways to prevent algae bloom, we must know how they reproduce. So let us start with that!

The environmental conditions that lead to the proliferation of algae are: 1) warm water temperature, 2) sunlight, and 3) abundance of nutrients.

If we will look at the three conditions above, these are also things that hydroponic systems require. This makes hydroponics a very favorable place for algae to grow and develop.

Now that we know these factors, we can now address them.

Secret Hacks for Warm Water

I have developed a habit of always checking my hydroponic water temperature. This is something that I also recommend. You can also monitor your growing room temperature by installing 2 to 4 thermometers around your hydroponic system. This way you can adjust the temperature if needed.

To adjust water temperature:

  • You can add cold water every 15 minutes until the optimum temperature of 18-21°C (64-70°F) is achieved.
  • You can also add ice packs into the water and remove them once the water temperature is back to normal.
  • You can also use water chillers.

To adjust room temperature:

  • Use an electric fan to increase ventilation in your hydroponic system.
  • You can also use insulators in the room to lower heat absorption.

Secret Hacks for Sunlight Exposure

Below are great ways to prevent unwanted sunlight exposure in hydroponics

  • Choose opaque hydroponic reservoirs.
  • Use opaque pipes.
  • If you have already bought clear or translucent pipes, hoses or reservoirs, you can paint the pipes and reservoir with a dark color that will lessen the amount of sunlight passing through them.
  • You can also use aluminum foil to wrap your transparent hoses.

Once these hacks are performed, algae will be unable to develop and compete with the hydroponic plants. This means the nutrients will not be consumed by algae and will be fully used by your hydroponic vegetables and herbs!

2. Overgrown Roots

When hydroponic roots grow too long and fibrous, they could hinder the proper flow of water in the hydroponic system; thereby making nutrient distribution inefficient.

Overgrown Roots Clogging
Overgrown Roots Clogging

Secret Hack: Clogging can be solved by trimming the overgrown root system and pulling out roots that have gotten into the pipe.

Follow the steps below when trimming your roots:

  1. Clean your trimming scissors using 70% ethyl alcohol.
  2. Carefully lift your plants until you see the roots.
  3. Trim the bottom ⅓ of the roots. Note: Prioritize removing discolored roots and avoid trimming the upper portion of the roots.
  4. Rinse the roots with water.
  5. Put them back in the hydroponic system.
  6. Circulate food-grade hydrogen peroxide by diluting 2-3 teaspoons to every gallon of water in the reservoir.

3. Loose Growing Medium

Having a loose growing medium can produce soil and dust debris. When debris accumulates, they can clog tubes of water and air pumps, affecting the delivery of oxygen and water throughout the hydroponic system.

This is a problem for growing mediums such as coco coir, perlite, and peat moss. Since they have small particles, they tend to disintegrate in the hydroponic system.

Secret Hack: Before transplanting the plugs into a hydroponic system, it is critical to first establish a strong root structure.

How to Prevent Clogging From Growing Medium
How to Prevent Clogging From Growing Medium

Look at the illustration above. When roots entangle the growing medium, there will be lesser chances that it will disintegrate and clog on your hydroponic tubes and hoses.

4. Suspended Solids in Emitters

Suspended solid particles are the most common cause of clogging in hydroponic emitters. This is a prominent concern for drip irrigation systems. These solid particles may be in the form of plant debris or sand particles.

For those of you who are not familiar with emitters, they are commonly used in drip systems. They are connected to a hose that delivers nutrient water to the plants in a precise manner.

Secret Hacks to Remove Suspended Solids in Drip Emitters

  • You can use a toothpick to remove clogged particles in drip emitters.
  • Blowing on them is also another way to remove sand or plant particles.
  • A high-pressure water spray can also be used to wash out particles present in emitters.
How To Clean Your Drip Emitters

5. Small Pipe or Hose Diameters

Small pipes in a hydroponic system are more vulnerable to clogging. Salt, minerals, debris, and algae can easily cling onto the interior walls of pipes and even air and water tubes.

If you have small systems with small pipes, I know that this problem seems to be a huge concern. But do not worry, I got you!

Secret Hacks for Salt and Minerals Blocking in Small Pipes

Salts and minerals are left when there is constant evaporation. But more than just controlling high temperatures, we should also address the possible sources of these blockers.

With this, I suggest using filtered water—not tap, soft, or hard water. Why? Because these water types have relatively high amounts of salts and minerals such as chloride, calcium, fluoride, and magnesium that can buildup and clog tight pipes.

   Head to our article about water types to learn more about this. 

Secret Hacks for Plant Debris and Algae Blocking in Small Pipes

To physically remove plant debris or algae, use a high-pressure water spray or a garden hose. But because these are both biological agents, simply removing them does not suffice. So there will be an additional step of disinfection after that.

Allow a diluted solution of hydrogen peroxide or bleach to pass through the pipes to accomplish this. You can also soak your pipes overnight in these solutions. This ensures that potentially harmful microorganisms associated with the debris are also removed from the system.

   Learn more about how to use these disinfectants in our article on hydrogen peroxide vs bleach. 

3 Problems Because of Clogging in Hydroponics

Clogging in hydroponics can adversely affect the hydroponics system by causing poor water flow, inefficient nutrient distribution, and salt buildup.

Negative Effects of Clogging in Hydroponics
Negative Effects of Clogging in Hydroponics

1. Poor Water Flow

When pipes and tubes become clogged, water flow becomes slower. As a result, the hydroponic solution cannot go to its intended path. For instance, in vertical nutrient film technique, there is a possibility that water could not climb upwards due to clogging.

Just like in a normal water faucet, clogging will lessen the flow of water. The same thing goes with every hydroponic system.

In ebb and flow systems, a reduction in water flow can disrupt the system’s flood and drain schedule, which is essential since it ensures that the roots receive oxygen and nutrient solution at the same rate.

 Discover more about this in our article about clogging in ebb and flow systems. 

2. Inefficient Nutrient Distribution

Since hydroponic nutrients are mixed with water, the poor water flow will also result in inefficient nutrient distribution. This is visible when only a portion of the hydroponic system produces healthy plants.

At this point, we can observe a chain reaction that will happen once clogging happens in a hydroponic system.

When there is a weaker flow of water, the dispersal of nutrients that come with it is also affected. Thus, there is a possibility that your hydroponic veggies and herbs will not get sufficient nutrients for their growth and development.

This could further result in curling of leaves, general yellowing of the plant, and further, withering.

3. Salt Buildup

When nutrients are not distributed effectively, the risk of salt and mineral buildup increase. This can be further caused by poor water flow along with a high temperature in the water reservoir.

The chain reaction continues…

Since there is poor distribution of nutrients, the hydroponic solution will become more stagnant. In this period, evaporation still happens. When water evaporates, salts and minerals from the hydroponic nutrients are left behind.

This will lead to salt buildup. This is the reason why it is important to take note of every single hack I have given throughout this article!


Which hydroponic system is more prone to clogging?

Pipes and hoses in hydroponic systems are prone to clogging. Systems prone to clogging include the nutrient film technique, the ebb and flow system, and the drip system. Because wicking and deep water culture hydroponics do not use tubes, they are not susceptible to clogging.

Why do hydroponic leaves curl?

Hydroponic leaves start curling as a result of a lack of water, oxygen, or nutrients delivered to the roots. As a result of the scarcity of resources in their cells, they curl to conserve them. Some reasons for scarcity include clogging in the hydroponic system, root rot, and algae infestation.

Summary of Hydroponic Clogging Problems

Clogging in hydroponic systems is usually caused by algae infestation, overgrown roots, loose growing medium, suspended solids, and small pipe diameters. When this happens, there could be poor water flow, thereby causing nutrient distribution inefficiency, and further salt buildup.

However, clogging can be prevented by providing the optimum temperature, blocking sunlight from reaching the nutrient water, trimming overgrown roots, establishing strong root structure before transplanting, and using filtered water.

Pipes, emitters, and hoses can be cleaned using a high-pressure water spray or garden hose. For biological blockages such as algae and plant debris, an additional step of disinfection using hydrogen peroxide or bleach is needed to prevent spread in the next growing cycle.


  • “Methodology to Evaluate Dripper Sensitivity to Clogging due to Solid Particles: An Assessment” by Lavanholi, R in The Scientific World Journal
  • “Be aware of the challenges of using loose substrates in hydroponic production systems” by Kuack, D. in Hort Americas
  • “Ebb & Flow Hydroponics Watering Schedule: How Often to Flood & Drain?” by n/a in Leaffin
  • “Sodium Hypochlorite to Hydrogen Peroxide: A Comparison” by COVID-19 CETA Technical Committee in Cleaning Equipment Trade Association

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