How to Troubleshoot Common Problems in Hydroponic Cannabis Growing

Growing cannabis hydroponically is awesome and comes with plenty of perks. Your plants experience faster growth and you get greater control over nutrients. But even with the benefits, hydroponics isn’t immune to its own set of challenges. Grow enough plants and you’ll have a list of common issues you’ll come across. 

Whether you’re dealing with wilting seedlings, nutrient imbalances, or pest invasions, each hydroponic issue requires a different approach to keep your plants happy and thriving. In this article, we’ll go over some common hydroponic cannabis growing problems, and most importantly, how to troubleshoot them so your plants stay healthy. 

1. Seedling Issues with Hydroponic Cannabis 

Starting cannabis seedlings in a hydroponic setup can feel like a balancing act. Your young plants are especially sensitive and, if conditions aren’t just right, they’ll be quick to let you know. 

Here’s how to handle some of the most common seedling problems you might encounter and keep your little cannabis seedlings. 

Are the Seeds Wilting?

A wilting seedling can seem like it’s giving up on life, and there are a few reasons this might happen. It may be due to not enough water, too much heat, or something else. When seedlings don’t have the right balance, they’ll lose their stiffness, and their leaves may start to look parched.

You need to make sure your roots have a chance to dry out a bit between waterings — hydroponic systems work best with balance. And just in case your water pump decides to go on strike, keep a backup pump ready.

Are the Roots Dying?

Dead roots in seedlings are usually a signal that something’s off below the surface. The water might be too warm, the EC (electrical conductivity) levels could be out of whack, or overwatering in a dense substrate could be the culprit. 

What can you do? 

If you find seedlings with dead roots, remove them from the system right away to prevent the problem from spreading. Then, adjust your water temperature and monitor EC levels closely. 

You should also maintain your setup. Regularly cleaning and sanitizing your setup is key to keeping pathogens at bay, and ensuring a healthy environment for your young seedlings.

2. pH Imbalances in the Hydroponic System

Getting the pH right in a hydroponic system is like finding the sweet spot for your plants to thrive. For cannabis, that optimal range is usually between 5.5 and 6.5, and when the pH strays outside these numbers, your plant can struggle to absorb nutrients properly. 

The result? Nutrient deficiencies, toxicities, and stunted growth. So, here are some tips that will help you keep the pH in check for your cannabis plant. 

• Monitor Regularly

Make it a habit to check your nutrient solution’s pH with a pH meter or test kit. A daily check is ideal but aim for at least every few days to catch any shifts before they become a problem.

• Adjust the pH When Needed

If the pH creeps out of the target range, you’ll need to bring it back. You can use a pH up or down solution to nudge it right where you need it. Usually, these solutions are stronger than household acids or bases, so applying a small amount will make a noticeable change.

However, be careful with them. Even a little extra pH up or down solution will change the pH significantly (especially in smaller systems). Add a few drops at a time, check the pH, and repeat if needed. This is even more important if you're working only on a small system. 

To prevent this problem, use droppers or syringes. If you pour the solution into the water, you won't be able to control the fluctuation and may have to start all over again. So, add one or two drops, stir, and recheck the pH until it is within the desired range.

Also, don't chase the pH because if you over-correct it, it will swing back and forth which is harmful to your plants. Small changes help you hit the right spot without big ups and downs. If you find it very difficult to adjust the pH when working with small reservoirs or if you want to change the pH slightly, you can just dilute it first and then use it. This isn't necessary in larger containers as you won't encounter huge changes. 

Also, once you add the pH adjuster, let it circulate through the reservoir for a few minutes so it can stabilize to prevent inaccurate readings. Also, there’s no need to adjust it instantly; instead, give it some time and the pH will stabilize gradually. 

If you're working on larger systems, you can use a pump to speed up the circulation. In addition, it will also improve the accuracy of the pH measurement as it will be distributed instantly throughout the reservoir. 

Finally, remember to stay away from household products to reduce or increase the pH. Many people suggest using lemon juice or baking soda but they won't work as much as commercial pH adjusters due to their instability and impurities. For best results, use pH solutions that are meant for hydroponics.

• Be Consistent

You must keep things steady by adjusting the pH regularly and keeping an eye on any fluctuations. Stable pH levels help your plants stay happy and stress-free, giving them the best chance to grow strong.

With a balanced pH, you’re setting up your cannabis plants for peak nutrient uptake and growth.

3. System Malfunctions: Air Pump Failure

Air pumps are super important in hydroponic systems as they oxygenate the root zone. If they start malfunctioning, it may lead to a host of problems, including nutrient deficiency and root suffocation. 

Hydroponic systems need air pumps that supply oxygen to the roots as they are submerged in water. However, if the roots don’t get adequate oxygen they can start suffocating. Thus, you need to have an air pump you can depend on to keep the plants healthy and happy. 

If you don’t take action quickly, it can even kill the plants. 

Symptoms of the Air Pump Failing

If the air pump fails, the oxygen levels drop and stress the plants. A common symptom of lack of oxygen is wilting or drooping leaves, and the plants appear very limp. You may also notice root rot where the roots turn brown and develop slime when they don’t have oxygen. 

Finally, plants that don’t get enough oxygen can behave as if they don’t have enough nutrients. For example, they may get yellow leaves and stunted growth caused by oxygen deprivation.

How To Fix Air Pump Problems

If you notice any of the above, do the following to troubleshoot the air pump problem: 

1. Check the Power

• Be sure the air pump is connected to the power line. Sometimes, plugs get loose or power strips get turned off accidentally.
• Check the outlet by plugging in another device or resetting tripped circuit breakers. If the power supply, as opposed to the pump itself, is defective, this step can help you fix it. 

2. Check for clogs

• Check the tubes and air stones for blockage. If any kinks or bends are found in the air pump and the air stones tubing, adjust it or change the tube as they can restrict airflow. Also, remember that with time, algae, minerals, or debris can clog the airlines and diminish oxygen output. In case of blockage, disconnect the air line and blow through it or use compressed air to clear the obstruction.
• Air stones can get clogged with nutrient salts or algae. Clean or replace them in case of clogging. Leave them for a few hours in a diluted vinegar or bleach solution before replacing them after rinsing well. If cleaning does not allow the airflow back, replace them to ensure oxygen diffusion.  

3. Check for Strange Sounds or Vibrations

• A properly working air pump makes a steady humming sound. It shouldn’t make other sounds like clicking, grinding, or banging which indicates that the parts may be getting worn out. 
• If it vibrates excessively, it might mean that the motor or other internal parts might be misaligned, or that the pump has shifted on its mounting. To fix this, simply put a foam pad or rubber mat under the pump to minimize the vibration and extend the life of the pump.
• If the pump is abnormally hot, that’s a bad sign and probably means it’s working too hard or close to failure as high temperatures typically signify that everything is not functioning as it should. 

How to Prevent Air Pump Failures

You can prevent pump failures with routine maintenance and proper monitoring. Here are a few things you can do:

• Clean the air stones and lines at least once or twice every two months to avoid clogs that can build up when there are algae or minerals. 
• Have a backup air pump so that you don’t get affected by the primary pump failure.
• Do not place the pump in excessive humidity and dust as this may cause clogging. 

If you follow these steps this will keep the air pump of your hydroponic cannabis system in good shape which will in turn ensure that your plants get the oxygen.

4. System Malfunctions: Water Pump Failure

The water pump, an essential component of a hydroponic system, is responsible for regulating the flow of nutrient solution to the plants. If it breaks down, the nutrients can’t reach the plants and the plants will experience nutrient deficiencies pretty rapidly. At this stage, the plants can begin to suffer stress or even get damaged. 

And, just like a failing air pump can show symptoms on the plants, you should watch out for symptoms like stunted growth as they aren’t getting enough nutrients. You may also notice the plant yellowing as it can no longer transport nutrients. 

If the water starts to stagnate, it can reduce the oxygen levels that encourage root pathogens and also increase the chances of root rot. 

How to Fix Water Pump Problems

If you detect any of the symptoms mentioned above, you may need to check the water pump.  

• Like you would with the air pump, check the power first and see if the problem lies in the pump or with the outlet itself. 
• Next, take a look at the intake filter and tubing for blockages due to any debris, leaves, and algae that may get lodged around the filter on your pump. This can interfere with water entering the pump and sometimes even block it altogether. Simply clean the inlet to clear blockages. Your tubing could be blocked with a mineral deposit, biofilm, or debris that builds up within the tubing. Take the tubing off and flush it out with warm water or vinegar solution for blockages.
• Also, make sure you clean the impeller. An impeller is a small rotor inside the pump that moves the water through the system. Like the tubes, it can also get clogged with nutrient salts, algae, and other particles over time. To clean it, take apart the pump carefully to get a hold of the impeller. If in doubt, look at your pump manual. You can use a diluted solution of vinegar to soak it or use a soft brush to scrub it. Wash it well before putting it back in. Be careful while assembling — all parts should be in the same place otherwise it may leak. 

How to Prevent Water Pump Failures 

• Have a backup

Just like the air pump, having an extra water pump as a backup can stop other damages from happening. A quick change can help your system continue working properly, which in turn helps save plants.

• Regular maintenance

Clean and check the pump and tubing of your system regularly to avoid blockage and mineral deposits.

• Environmental conditions

When installing your pump, you should avoid areas that are too humid or dusty. A humid area will wear, or leave dust in sensitive parts.

5. Your Cannabis is Experiencing Nutrient Issues

Nutrient deficiencies can sometimes be a headache in hydroponic setups, as symptoms might not always tell the whole story. So, before jumping to conclusions, you should check your water temperature, nutrient solution pH, and the solution’s electrical conductivity (EC). 

If those are in the ideal range, then it's time to take a closer look at the nutrient composition to make sure your plants are getting what they need.

The unfortunate part is that your plant needs a lot of nutrients and it’s not always easy to figure out exactly which nutrient (or lack of it) is the culprit. So, you need to take the symptoms into account and figure out which nutrient deficiency your plant may be facing. 

We’ve written many articles on specific nutrient deficiencies that you can refer to. Remember to cross-check the symptoms and use the recommended remedies to fix that particular nutrient deficiency in your cannabis plant. 

Fortunately, hydroponics simplifies many aspects of cannabis cultivation, but each solution depends on how well you handle these unique challenges. No matter how intimidating a problem might seem, there’s usually a practical fix.

6. Your Cannabis Roots are Rotting 

Root rot is a grower’s nightmare — it sneaks into hydroponic systems via pathogens that compromise your plant health from the ground up, often spreading quickly. It’s always better to know what causes root rot, which is the first line of defense. 

Here are some of the common causes of root rot in cannabis plants:

• Pests like Fungus gnats and other critters can bring pathogens directly to your plants
• Introducing new plants that haven’t been properly checked or cleaned can spread infection fast
• Some pathogens lie dormant, waiting for the right conditions to wreak havoc on your roots

If your cannabis plant is facing root rot, you can try washing the roots to remove the rot. However, in some cases, flushing the roots may not work. Instead, you need to prevent it in the first place, and here’s how you can do that:

1. Maintain your nutrient solution temperature below 75°F (24°C) to keep pathogens at bay
2. Proper oxygenation helps prevent root rot by keeping roots healthy
3. Regularly clean your hydroponic system and tools to limit exposure to pathogens
4. Use dark or thick materials to keep light away from the root system; light exposure can promote algae, which may fuel root rot

Regular checks and smart prevention will keep your cannabis plant happy and thriving, letting you stay ahead of root rot before it sets in.

7. There are Pests on Your Cannabis Plant 

Even in hydroponics, pesky invaders can still make themselves at home. Since these pests are just as happy living without soil, it’s essential to keep an eye out for any signs of infestation and nip them in the bud — pun intended! Let’s look at how you can deal with them.

First, all-natural insecticides are a great first line of defense. Options like neem oil, garlic oil, and vinegar are safe and effective for deterring most pests. Organic insecticidal soaps are also highly effective at keeping pests under control without harming your plants.

You can also use beneficial bugs, which can be your garden's best friends. Introducing critters like ladybugs or predatory mites will help keep pest populations in check, making them the pest control you didn’t know you needed.

Finally, create an unwelcoming environment for the pests. Avoid conditions that pests love, like slime, algae, and damp areas. Proper airflow, clean water, and a dry environment help keep pests and pathogens from making a home in your garden.

With a little diligence, you can maintain a pest-free hydroponic setup that lets your cannabis plants grow strong and stay healthy.

8. Your Hydroponic System is Clogged

With hydroponics, where water flows are essential, system clogging is a frequent issue. This is why you should know your system inside out and regularly inspect for any signs of breaks or leaks. This can save you from bigger headaches down the line.

Apart from the blockages in the air and water pumps, you'll also have to be careful about the blockages in drip systems as they are prone to them. Even ebb and flow systems suffer the same fate. As time goes on, these systems can become obstructed by salt formation, nutrient sediment, root bits, or bio-film — a slimy bacterial formation. That's why it's important to take care of these blockages to ensure nutrients are delivered consistently to the plant.

Causes of Blockages

• The nutrient solution evaporates, leaving behind salt and minerals that build up in the tubing and emitters. High nutrient concentrations or the presence of hard water further aggravate it. 
• Nutrient sediment refers to little particles that do not dissolve, which occur mainly in high-dense nutrient solutions. They can settle in the tubing, blocking pretty much everything. 
• In ebb-and-flow systems with close root access, root fragments can enter the lines, block them, and further spread root diseases.
• When the heat or light exposure is high, algae and biofilm grow inside the tubes and emitters, creating a slimy blockage that restricts the flow of water.

Signs of Blockages

Let's assume you've taken care of the pH, and water quality, haven't over or under-watered, and are supplying nutrients properly. But, what do you do if your plant still shows signs of nutrient deficiency and refuses to grow properly? 

Well, this could be a symptom of a blockage as the nutrients may be getting distributed unevenly or the plants may not be getting anything at all. You may also notice a buildup of salts or residue that appears as white and crusty spots on the emitters, dripline, or tubing which is a sign of a blockage. 

If the water flow appears slow in specific lines or emitters, there is likely a partial blockage.

How to Clear Blockages

1. Flush the system

• Make sure you run plain water through the system for some time to flush any loose debris and sediment.
• Use a mild vinegar solution to dissolve mineral deposits and salt accumulation. After that, rinse thoroughly with clean water to remove the remaining residues. 

2. Check Drip Lines and Emitters

• Take them apart and check for visible clogging in the drip lines and emitters.
• For a minor blockage, use a thinner wire or a needle to clear the obstruction. However, be careful not to damage sensitive components because even a small hole or crack in them can worsen the problem. 
• Replace emitters that are severely clogged or damaged to restore complete water flow.

3. Clean the system thoroughly

• Take apart the lines, emitters, and tubes that keep getting clogged and soak them in a mixture of bleach and a commercial cleaner or anything that makes cleaning easier. 
• To kill bacteria and dissolve mineral buildup, soak these parts in a diluted bleach or hydrogen peroxide solution for several hours. Before putting them back together, rinse them well to avoid exposing the plants to chemicals.

To confirm the smooth flow of water through all lines, test the system flow after reassembly.

How To Avoid Clogs

• Flush the system at least once after every harvest with plain water or a weak solution of vinegar and water  
• Install some pre-filters at the intake to capture larger particles and prevent them from entering. This is beneficial as it stops the clogging of drip lines and emitters.
• Making the nutrient reservoir and tubing light-proof can help to reduce algae growth, which otherwise can make these transportation lines slimy.
• Make sure to use quality, fully soluble nutrients to avoid sediment buildups and keep the lines clear. 

9. Not Enough Air Circulation in Your Setup

Good airflow is essential to maintaining a balanced environment for your cannabis plants. Fresh air supports photosynthesis, respiration, and temperature regulation in your garden. Without it, your plant won’t thrive much.

What can you do if the air is not circulating well in your hydroponic setup? Add a few fans — this will make a big difference in the air movement and help keep mold at bay. You can also add computer fans or oscillating fans to keep the air circulating in your grow room. 

10. Water Quality Issues

When growing cannabis hydroponically, using high-quality water is essential. This is because the plant relies on the nutrient solution for growing well. Poor water quality can kill plants or restrict their growth and lead to nutrient deficiency, blockage, and other health concerns. Therefore, keeping water clean and balanced is essential for the healthy growth of plants.

Clean water is crucial, especially when you're growing cannabis hydroponically. 

The basic principle of any hydroponic system is water quality. Hydroponic plants are very sensitive to the quality of the water as they take everything directly from the solution. The plants’ ability to absorb nutrients is better when water quality is improved. Too many contaminants or imbalances can cause nutrient lockout or unavailability of nutrients.

If a hydroponic system does not receive enough nutrients, problems may arise because of the blockage of algae or particles in the water forming tubing, emitters, and filters.

Clean water will also prevent pathogens, bacteria, and algae from developing. So, basically, the source of water you use will determine whether it contains contaminants or not. 

Many people use tap water, but it typically contains chlorine and chloramine that can affect hydroponic cannabis plants. To prevent this, let the water sit in a bucket for a day (24 hours) to let chlorine dissipate. 

For your peace of mind, you can use filtered water if you’re not happy with the water you’re using. Some growers also use RO water. 

11. Algae and Biofilm Formation

Algae and biofilm are very common in hydroponic systems but you can manage them easily. 

Algae is a photosynthetic organism that requires light and nutrients to grow, so nutrient reservoirs and nutrient tubing that are exposed to light can become breeding grounds for algae. 

On the other hand, biofilm is a matrix of bacteria that coats surfaces in a slimy coating. In addition, algae and other organisms can also reside within biofilm. They can cause many problems for the health of plants and the system. 

To control algae, it is important to identify them early. They typically appear as green or brown slimy patches along surfaces exposed to light. You can see them on the inner walls of reservoirs or tubing. Brown algae isn't very common but it can appear in systems with unfiltered tap water.

Biofilms are often not visible to the naked eye. Instead, they appear clear and slimy or cloudy. You will usually notice it when you touch it as it's slick. The only problem is that it starts blocking water from flowing through your tubing or emitter devices.

How Algae Affects Plant Health

Algae can be harmful to plants both directly and indirectly. They fight for nutrients, particularly nitrogen, phosphorus, and other macronutrients which hinder the growth of the plant.  When they grow without interference, they compete with plants for these and cause deficiencies.

In addition, algae and biofilm consume the dissolved oxygen present in the water, meant for the roots. As the levels reduce, the roots can get stressed. 

Algae and biofilm also create favorable conditions for pathogens, particularly Pythium (root rot), Fusarium, and other fungal pathogens. The organic matter that accumulates allows these pathogens to thrive. 

Finally, the algae feed on carbon dioxide during the day and release it back at night causing fluctuations in the pH level. The problem varies as per weather, and with time, there will be too many complications in pH.

How to Avoid and Remove Algae

• First off, keep your system clean and algae-free by being consistent.
• Prevent algae growth by covering all water-exposed parts of the system, as they thrive in light.  This involves using opaque containers and/or wrapping transparent tubing with dark tape or reflective tape.
• Scrub the area well to remove any algae. Regularly check for light leaks and fill any cracks or gaps to keep it light-proof.
• Algae and biofilm thrive in warm water. Thus, aim for water temperatures between 65–70°F (18–21°C). This temperature is good for cannabis roots but not for algae.
• Use a water chiller to cool down the nutrient solution when using very high-intensity lighting or in warm climates, where temperatures can easily get high. Insulated reservoirs can help in lowering temperatures.

Maintenance of Hydroponic Systems

Regular upkeep is vital for hydro systems to function smoothly and for all the equipment to work optimally. Taking proper precautions can help your equipment live longer and will also prevent any unexpected breakdowns that can hamper plant growth. Here's how you can ensure your systems last for a long time:

1. Clean and Sterilize

• There's no way around this — you must clean your system regularly to maintain the quality of the water so there are no pathogens that can contaminate the water. This will also prevent blockages. 
• Empty and clean the nutrient reservoir every one or two weeks and wash all the components one after the other. This stops algae, mineral buildup, and nutrient residue that can damage equipment and water quality.
• To kill bacteria, algae, and fungi, you can use a sterilizing agent (hydrogen peroxide or diluted bleach) after rinsing. Wait for parts to air dry to refill with nutrient solution to avoid exposing the plants to harsh chemicals. However, don't wait too long or the roots may dry out. 

2. Regular Inspections

Regular inspections prevent minor issues like cracks, leaks, or blockages from becoming bigger problems. Keep an eye out for noises, vibrations, and visible signs of problems with pumps and hoses. If hoses and pumps show cracks or brittleness, replace them.

3. Swap Out Parts

Air stones, filters, and tubing wear out and need to be replaced quite often. Replace the air stones every 2-3 months as they become too clogged with mineral deposits and will not oxygenate the nutrient solution as needed.

Clean or replace the filters and tubing every few months as they may trap particles and have sediment build up. Using fresh tubing reduces the chance of leaks from brittle tubing.

Over time, the emitter will clog, limiting how much water can flow out. Change these parts after a few months for the best performance.

4. Keep an Eye on Electrical Connections

• Electrical components are essential but sensitive parts of hydroponic systems. If you are careful and vigilant, there will be no short circuit.
• Examine power strips and outlets for moisture as it can prevent accidents. Keep electric devices off the ground and away from water.
• Ensure that all cables and connections are intact and not going to become a trip hazard or dripping. Make sure the connections are tight and free of corrosion.

Summary: How to Troubleshoot Common Problems in Hydroponic Cannabis Growing

While growing cannabis hydroponically comes with its own set of challenges, you must take a proactive approach to troubleshoot and fix the issues. This can make all the difference.

You must start by monitoring for early signs, adjusting setups when needed, and maintaining a clean environment. Only then can you tackle each issue effectively. With regular checks and care, you’ll have a flourishing, high-yield garden that benefits from hydroponics’ advantages while avoiding most problems.