Clogs in your Grow Room

Clogs in emitters, feeding lines and drains

One of the biggest challenges growers face with irrigation systems is clogs. Clogs can form from physical particles, chemical precipitates or biological growth, and they can occur in an irrigation system’s lines, emitters or drains. Not only do they prevent the irrigation system from functioning properly, but they can also be detrimental to crop health and yield.

Figure 1

Consequences of clogs

Clogging in is more than a maintenance nuisance. Because clogs reduce the uniformity of water and the nutrient solution, they can cause nutrient deficiencies or drought stress, which in turn can reduce yields and crop quality. They also increase the risk of pests and pathogens[1] and reduce the efficiency of the irrigation system, which can shorten its lifespan.

Types of clogs

Clogs can be broadly classified into three types: physical, chemical and biological.

According to the statistics of a consultant from the Food and Agriculture Organization, biological clogs are the most prevalent, occurring with a probability of 37% in drip-irrigation emitters. Physical clogs are the second most likely to occur at 31%, while the probability of a chemical clog is 22%.[2]

Biological clogs

Biological clogs, also called biofouling, happen when conditions favorable for the rapid growth of microorganisms such as fungi, algae and bacteria occur inside the irrigation system, resulting in a slime called biofilm.

Biofilm is a viscous layer composed of bacteria and organic polymers knowns as extracellular polymeric substances (EPS), mainly polysaccharides and proteins that allow the microorganisms to adhere to surfaces within the irrigation system. Microorganisms develop biofilm in reaction to various factors, including specific or nonspecific attachment sites on surfaces.

Not only does biofilm adhere to surfaces in irrigation systems, but it also surrounds itself with a protective structure and can attract other suspended particulate matter. Some bacterial species can even cause the precipitation of iron, manganese and sulfur compounds dissolved in irrigation water, further contributing to clogs.

Biofilm reduces oxygen in the water and can foster and harbor harmful pathogens. Research suggests at least two-thirds of waterborne pathogens come from biofilm.[3]

Physical clogs

Physical clogs result from particle residues, sediment and fragments in irrigation water. They may originate from sources such as debris or organic matter in the water supply. If growers use poor-quality irrigation water or a filtration system that is poorly designed or installed, these particles may get pumped into the pipeline. As they pass through irrigation lines and emitters, they settle and form deposits, eventually restricting water flow. The higher the concentration and size of these particles, the more likely clogs will develop.

Figure 2 The types and probability of emitter clogs. Source: Shi, Kaili, Tiangang Lu, Wengang Zheng, Xin Zhang, and Lili Zhangzhong. 2022. “A Review of the Category, Mechanism, and Controlling Methods of Chemical Clogging in Drip Irrigation System” Agriculture 12, no. 2: 202.

Unfortunately, physical clogs can occur even when using high-quality water. Sometimes corrosion and scaling in the irrigation system contribute to physical clogs, as mineral deposits and rust may accumulate on the inner surfaces of the pipes.

Chemical clogs

Soluble substances in water sources—such as carbonates, phosphates, sulfates, silicates, hydroxides and so forth—can form chemical precipitates under certain conditions, resulting in chemical clogs. These types of clogs take a long time to accumulate and do not occur suddenly.

The irrigation system’s pressure, water temperature and pH, as well as the concentration of ions in the water, influence the formation of chemical clogs. Fluctuations in pH levels can trigger chemical reactions that form precipitates, while water temperature changes can impact the solubility of ions and minerals in the water and cause them to precipitate.

Fertilizers can also cause clogs if they react with other fertilizers or pesticides in the solution or with minerals in the water and form precipitates.[4]

Table: Factors that lead to chemical clogging[5]
Induced factor


Severe clogging is likely to occur when water pH is higher than 8.


Iron can cause severe damage to irrigation systems at high concentrations.

Hydrogen phosphate and phosphate

Fertilizers with high phosphorus can lead to chemical precipitation in emitters.

Calcium ions, magnesium ions, and bicarbonate

If irrigation water contains high concentrations of calcium ions, magnesium ions or bicarbonate, particularly in fertigation, the risk of emitter clogging increases. When the pH of irrigation water is greater than 7.5 and the bicarbonate content is greater than 5 mmol/L, more scale is likely to form.


Clogging occurs if manganese exceeds 0.1 mg/L, and it is aggravated if exceeds 1.5 mg/L.

Hydrogen sulfide

Clogging occurs if hydrogen sulfide exceeds 0.5 mg/L, and clogging it is aggravated above 2 mg/L.

Preventing and controlling clogs

While biological clogs are more prevalent in recirculating systems, and physical and chemical clogs are the primary concerns in freshwater irrigation, a combination of all three—called composite clogging—is not uncommon in standard drip irrigation systems.

Growers can take several measures to keep clogs from wreaking havoc on their irrigation systems:

  • Filters and screens can prevent physical clogs caused by solid particles. Install high-quality filtration systems to remove particulate matter and debris before it enters the irrigation system.
  • Maintain water pressure by installing a pressure gauge. Too low—or surprisingly, even too high—water pressure increases the risk for clogging.
  • Check for fertilizer compatibility when mixing and matching fertilizers. This is not a concern if you are using Emerald Harvest, as our base nutrients and supplements are compatible with one another.
  • Periodically flush the system with clean water to remove accumulated debris, salts or residues that can cause clogs. This may reveal the presence of biological growth in the lines; in that case, flushing with chlorinated water may be required.
  • Use enzyme-based cleaners to tackle biofilms, such as Emerald Harvest’s Hydra Clear.
  • Acidify the irrigation system if you find mineral precipitates are flaking off the pipes. Acidification helps to dissolve any chemical precipitation.
  • Regularly remove dead plant matter from the root zone to reduce the risk of organic-matter buildup and minimize the nutrients available for microbial growth.
  • Regularly test water quality to identify any contaminants or impurities in the nutrient solution. Addressing water quality issues promptly can prevent chemical clogging and ensure the long-term health of the irrigation system.
  • Monitor and maintain optimal pH and electrical conductivity (EC) levels in the nutrient solution, as fluctuations in both can contribute to chemical clogging by promoting the precipitation of minerals and salts.

By taking preventive measures and clearing out any matter before it builds up, growers can keep clogs at bay and ensure their irrigation systems are running smoothly.

[1] Biological clogs deoxygenate the water supply, creating a favorable environment for anaerobic pathogens.

[2] Shi, Kaili, Tiangang Lu, Wengang Zheng, Xin Zhang, and Lili Zhangzhong. 2022. “A Review of the Category, Mechanism, and Controlling Methods of Chemical Clogging in Drip Irrigation System” Agriculture 12, no. 2: 202.

[3] Al Zylstra “You’ve Got Biofilm” GrowerTalks (2014); accessed January 30, 2023,

[4] Jatana BS, Sanders III TG. Micro-Irrigation System Maintenance to Prevent Clogging. Clemson (SC): Clemson Cooperative Extension, Land-Grant Press by Clemson Extension; 2024 Mar. LGP 1190.

[5] See Figure 1.

The Emerald Harvest Team

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