Challenges of Hydroponics Farming and how to overcome them 

Challenges of Hydroponics Farming and how to overcome them 
Hydroponic Cultivation

Shahbaz Khan

Hydroponics Technician - Agronomist

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I am confident writing this article because whatever I am going to mention is 100% from my experience, and I am very thankful that I have made many mistakes while growing plants with hydroponics over the years.

Hydroponic cultivation requires more technical skills than growing plants in soil. Plenty of information is available in books and articles and watching instructional videos. However, one of the best ways to learn is from my mistakes. 

I have put together this article about the most common issues you may experience. Hopefully, this information will prevent you from making some mistakes and give you the knowledge to deal with others successfully.

1. Leaks in Hydroponics systems 

Leaks in the system occur due to many reasons. Leaks can occur at any joints or valves. The most common leak problem I faced in my NFT system, i.e., the root mass clogs in the outlet point of the channel, and the system gets blocked, leading to water backing up and overflowing. It will cause serious issues when the algae forms in your NFT channel; the algae will observe the nutrient from the solution and show a Nutrient deficiency in plants.


Test your system before planting. Tighten any valves and make sure all connections are tight and secure.

Regularly check your system for problems such as root overgrowth or clogged drains or outlets; you have to do regular NFT leak maintenance. 

If you are using an indoor system, consider placing it on a waterproof surface or, if possible, on a drip tray if you are using a small system. This is a good idea to catch leaks, and it will also reduce mess when tending to your system.

Tips:- If you Grow Basil in the NFT system, prune the roots after 30 in indoor hydroponic systems

2. Selection of lighting in indoor hydroponic systems

I like to use my hydroponics system indoors to grow fresh vegetables all year round. The proper selection of lights can lead to the proper growth and production of plants. 

I make many mistakes with selecting light, such as buying the wrong type of light or using led light that is not in the correct wavelength will directly affect poor fruiting and uneven growth of plants observation and will affect your yield.

Solution :

Ensure you purchase enough grow lighting for your system. A good rule of thumb is to calculate the square footage of the canopy (growing area) of your grow area and multiply this by 65.

Here is a quick example;

A growing area of 4ft by 6ft. Total area = 24 sqft.

24sqft x 65 = 1560 watts

You will need approximately 1560 watts of grow lighting for this growing area. This is a good rule of thumb and is what I usually stick to.

For most cases, I recommend looking at LED and T5 fluorescent grow lights. These are typically the easiest to use and will be suitable for most users.fertilization in hydroponics

3. Wrong selection of fertilizer type and concentration

In hydroponics, fertilizer plays a crucial role in maintaining the plant’s healthy, growth, and productivity. However, we usually use a fertilizer unsuitable for hydroponic systems. Cultivating in the soil is a totally different situation, and another type of fertilizer is needed. 

In the market, there are numerous low-quality, cheap and unsuitable fertilizers, which will affect the hydroponic system and crops growing there.

Solution :

Make sure your purchase fertilizers for hydroponics that are 100 % water soluble and offer a balanced nutrient status/availability to your crop.

If you are running a commercial hydroponics project, select and get an expert’s advice and design your nutrient solution according to your crop and season.

Because the fertilizer selection per season is very different in hydroponics, here is my personal experience for one year.

For Example :

In the same plant, the uptake of nutrients is different in winter and rainy seasons as well as in irrigation expect, so be careful for commercial projects.

I recommend using Nutrient A and Nutrient B*, which are easily available in the market.

*In hydroponics, we used to call Tank A and Tank B. This is a Stock solution tank where different elements are mixed by experts.

Tips:- You can use a 19:19:19 (N:P: K) fertilizer for home gardening vegetables.

4. Hygiene Protocol

As per my experience in hydroponics, you can keep your plants safe by applying several hygiene measures/protocols. This is essential for cultivation in protected environments and especially for hydroponics farming. 

If your hydroponics farming area is dirty and messy, it may attract pests and pathogens and create a favorable environment for infestations and infections, putting your plants at risk.


A strict protocol for good hygiene inside and outside the greenhouse should always be followed. Keep the area around your facility clean and well-organized.

The workers or anyone entering the greenhouse should wear protective clothing (shoes, gloves, robes, etc.) to decrease the risk of transmitting pests and diseases from the outside to the inside of the greenhouse and from one area or facility to another. 

It is important to clean the NFT channels in every cycle, flush the growing media roots, and properly sanitize the reservoir once a month to kill any bacterial infection or wrong nutrient effect on plants.

5. Pest scouting

I learned from experience that this task would ensure 50% of the success of your hydroponics farming. One of the essential parts of hydroponics is to observe your plants frequently and detect in time the early symptoms of an infestation, infection, or nutrient deficiency (or toxicity). You can capture the symptoms in a picture or/and take a sample for analysis to facilitate the diagnosis and define the correct control measures. 

When you can find the problem early, it will have less effect on your plants.

5. The role of pH

The pH of your nutrient solution is one of the most crucial aspects of hydroponic cultivation. When growing plants in soil, the soil itself acts as a pH buffer and prevents rapid changes in the pH level. This means that the problems deriving from the pH will be less intense and develop slowly.

This is not the case for hydroponics; the pH can change considerably over hours or days due to many factors (including temperature, rate of absorption of nutrients by your plants, presence of disease, excess evaporation, etc.).

Solution :

As a result, we need to check the pH levels regularly; it mostly matters in the NFT, aeroponics, and DWC systems. You may need to test and adjust the pH daily in a new system or when recent changes have been made. You can reduce testing to once or twice weekly in a stable system. As you gain experience, you will begin to understand the factors that can influence the pH and get a feel for how often to test.

The best options for testing pH are to use a pH testing kit or a pH testing meter. I generally recommend getting a decent-quality electric pH testing meter, as it makes pH testing quick and easy.

6. Use of normal tap water in hydroponics

Hydroponics farming depends on water to give the plants an actual concentration of nutrients. You will likely be able to use tap water without significant problems, but tap water with a high level of total dissolved solids and salts will cause issues with your nutrient solution.

If the electric conductivity of your tap water is below 0.5 (200 ppm)(ideally, plants perform best when EC is between 1.5 and 2), then you can use it in a hydroponics system, but it should be constant. Otherwise, it will damage the plant roots.

High calcium concentration is common in tap water. Due to the high calcium slats that are gathered, the plants cannot absorb the calcium, and they start to show deficiency symptoms.

Solution :

The most common method used (and I personally use it on my farm) is a filter to purify the water, and the most successful is a reverse osmosis filter. Still, it is a more expensive option but will reduce dissolved minerals to zero.

Tips: If your tap water is less than (200 ppm) you can use it.

7. Role of PPM (Parts Per Million) /EC (Electric Conductivity) /TDS (Total Dissolved Solids)

The presence of salt in Nutrient solution is measured in PPM/EC/TDS. Continuous monitoring of TDS provides information on the nutrient concentration in the water. It can help you adjust nutrient levels to ensure that your plants receive the proper amount of nutrients for healthy growth.

Solution :

Use an EC/PPM/TDS meter to monitor the nutrient solution, both when making up the nutrient solution and over time as your plants grow.

Maintaining the EC/PPM/TDS in the nutrient solution, the plants continuously uptake the nutrient, and the nutrition decreases. They measured the solution through the meter and recharged the nutrient solution.

Change the nutrient solution after 3-4 weeks. This must be done, as the proportions of the various nutrients will deviate from the starting concentration due to variable take up by the plants.

8. Choosing the suitable growing media 

The selection of the right growing media is very important, and there are many factors to consider when choosing. It directly depends on crop and system selection.

Some crop performs very well in the NFT system, and it is easy to get ROI (Return Of Investment). However, the same crop cannot give good growth in the drip system, and it will fall to failure of the crop.

Solution :

The answer is difficult for the new grower, but here, as per my experience, because it took me more than two years after my search, I can give you this answer.

Crops are Lettuce, Basil, kale, Swiss chard, and rocket leaves perform very well with growing media oasis cubes in NFT System.

Crops of bell pepper, tomatoes, and cucumber performed very well with cocopeat substrate in a drip system.

9. Choosing the right Hydroponics system

There is a crucial role played in the selection of systems as per the crop. It depends on the size of your operation, budgets, and the level of automation in the hydroponics farms.


The system should be as per the selection of sites- availability of land – rural and urban areas- 

Market analysis – As per my experience, I grow multiple crops in different hydroponics systems. I am advising as per my experience.

NFT System: Lettuce, Basil, Kale, and Swiss chard

Drip system: Bell peppers, Tomatoes, cucumber and Zuckni

DWC system: Lettuce 

Aeroponics system: lettuce, Basil, rocket leaves

Ebb and Flow system: mainly used for seedling Preparation

Check the author’s article to learn more about the type of hydroponics system.



Read more:

A Beginner’s Guide to Hydroponics Farming: From Seed to Harvest

Different types of hydroponics systems and how they work

Challenges of Hydroponics Farming and how to overcome them


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