It’s time for a speed round of hydroponics troubleshooting. While hydroponic systems are relatively easy to work with, it doesn’t mean this cultivation method isn’t prone to a few common cultivation issues.
Most hydroponic problems revolve around nutrient imbalance or pathogens sneaking into the system. But, no matter the root cause, it is possible to address many common hydroponic problems without having to rip out plants and start from scratch.
Let’s tackle a few of the hydroponic issues you will most likely encounter in your indoor setup, starting with algae.
Addressing the Inevitable Algae Bloom
At some point in your hydroponic journey, you will have to troubleshoot an algae bloom. In a wet, warm, and light-filled environment, algae growth is inevitable.
You’ll likely notice green, red, or even black algae develop in the channels, nutrient tanks, and around the PVC piping. Long stings of growth will form, an earthy or moldy smell will develop, and as it dies off, your water will start to get murky.
Algae growth proliferates quickly, literally clogging up the works and sucking up much of your valuable nutrient solution. Unfortunately, it will also happily gobble up the crucial oxygen within your system. Without oxygen and nutrients, algae will slowly suffocate and starve your plants.
Because algae is a photosynthetic plant, it feeds in part off of light (which are already providing to your actual crops). So, one way to reduce the risk of complete algae takeover is to use dark and opaque materials for the piping, nutrient reservoir, and any channels where the water flows.
That means lids on your DWC buckets and a dark cover for your flood and drain the reservoir. Black tubing and opaque PVC piping will also help.
Between cycles, always perform complete sterilization and sanitization of the system, including the reservoir and piping. This will eliminate leftover algae and prevent its rapid regrowth in the next round.
Taking Notice of Burnt Leaves
If you start to notice discoloration and crispiness at the leaf ends, this is a key indicator your plants are suffering from nutrient toxicity. Also known as nutrient burn or tip burn, it’s related to elevated levels of nutrients within your solution.
If you have too much fertilizer in the nutrient solution, plants don’t have a stop mechanism. If the parts per million (ppm) is too high of one or all the nutrients, plants will continue to absorb them through the roots —until they absorb toxic levels.
Addressing tip burn starts with checking the electrical conductivity of the nutrient solution. Next, flush the system for at least 24 hours with pH-balanced water. Finally, before adding new nutrient solution, double and triple check the nutrient labels for dilution ratios. To make it easy, follow an established nutrient solution recipe when you are ready to re-apply.
Grower Tip: HydroGuide offers brand-specific nutrient recipes through our Grow App to help eliminate the guesswork and avoid nutrient burn.
HydroGuide
Plants are Stretching Out
Many aspects of the indoor environment can encourage (or discourage) your plants from stretching. Usually, as an indoor grower, you want to produce dense, bushy plants that pack a lot of flower into a small space. But what happens if your plants begin to stretch with too much room between each leaf node?
First, you’ll have to assess your environmental conditions. For example, your lights may be too far from the canopy or may not produce the right spectrum of color. Your plants may also be too close together, making for fierce competition to get in front of the light.
You can also employ specific pruning techniques that reduce stretching. These include pinching, training, and manually inducing stress. Many pruning and training techniques are specifically designed to promote bushing over stretching.
If your plants are stretching and you are well into the vegetative stage, it may be too late to make any significant adjustments. However, you can troubleshoot the issue in this round and adjust for the next.
Reducing Risk of Root Disease

Root rot is the bane of many hydroponic growers’ existence. This disease is a result of bacterial and fungal pathogens proliferating throughout your system. A host of different pathogens, perhaps more than 20, can lead to root rot, but the symptoms are generally the same.
These microscopic pathogens enter your grow room at any point: in the air, on purchased clones, on unsanitized tools, and even on your clothing. So unless you operate a completely sterile grow room, which is unlikely for a home set up, the best way to avoid root rot is to cultivate healthy plants and maintain vigilance.
Look for slimy, smelly roots. Inspect the roots of each plant in your system regularly to ensure they are white, clean, and healthy. Discolored and mushy root systems are a sure sign there is a system-wide issue. Plants with an advanced stage of root rot may begin to wilt, display discoloration as well as stunted growth.
Control for root rot starts with routine root inspection. Remove any infected plants, and complete a system flush. Root rot may also be a sign that there is a lack of oxygen, which means checking the function of each air stone or adding more should your system need it. Between each grow, always perform a complete system sanitization and sterilization.
Troubleshooting Hydroponics: Check the Nutrients and Keep Cleaning
Most common hydroponic problems can be course-corrected through adjustments to the nutrient solution and/or complete sterilization of the system.
But, most critically, it’s daily inspections on your hydro system that count. Check the nutrient reservoir, inspect the foliage, and carefully look at root systems. If you catch an issue early, you can usually solve it quickly. Remember, root rot and algae blooms don’t just appear overnight. They take a while to build up.
Keeping a close eye over your hydroponic system will help reduce the risk for most of the most common hydroponic issues.