Hydroponic Troubleshooting: Fix Root Rot, Algae, Nutrient Problems & More
Table of Contents
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How to Diagnose Problems
Before you panic, follow this systematic diagnosis approach:
Step 1: Observe the Plant
- Yellowing leaves? Check nitrogen/magnesium
- Brown leaf tips? Potassium deficiency or salt buildup
- Stunted growth? Root issues or inadequate light
- Wilting despite wet roots? Root rot
- Holes in leaves? Pests or calcium deficiency
Step 2: Check Your Equipment
- pH: Test with meter. Should be 5.5-6.5 for most plants
- EC/PPM: Test with EC meter. Should match plant requirements
- Temperature: 65-75°F (18-24°C) optimal. Too hot = low oxygen, too cold = slow growth
- Water Level: Adequate height in reservoir?
- Pump/Air Stone: Running properly? Listen for gurgling
Step 3: Inspect the Roots
This is critical. Root color tells you everything:
- White/Cream Roots: Healthy. Good oxygen, no disease.
- Brown/Black Slimy Roots: Root rot. Bacteria thriving in low-oxygen conditions.
- Red/Pink Roots: Phosphorus deficiency or early stress
Root Rot (Most Common Problem)
Root rot kills more hydroponic systems than anything else. But it's preventable and fixable if caught early.
⚠️ Root Rot
Diagnosis Signs:
- Mushy, slimy roots (brown/black, not white)
- Foul smell from reservoir (rotten/sulfur smell)
- Plant wilts despite wet conditions
- Yellow/brown leaf discoloration starting from stem
- Stunted or no growth for 1+ weeks
- Black streaks inside stems
Solutions (in order of effectiveness):
- Immediate: Increase oxygen. Lower water temperature to 65-68°F. Add air stone if absent. Increase air pump power.
- Remove Dead Roots: Drain system. Carefully remove plant. Cut away all black/slimy roots with sterile scissors. Keep white roots intact.
- Full Water Change: Drain completely. Rinse all system components. Refill with fresh water + nutrients. Check pH/EC.
- Add Beneficial Bacteria: Root rot is caused by pathogenic bacteria. Use beneficial bacteria supplements that outcompete pathogens.
- Hydrogen Peroxide (Last Resort): Add 3% hydrogen peroxide at 1ml per 1L water. Kills bacteria but also damages beneficial microbes. Use only if other methods fail.
- If Severe: Plant may not recover. Start fresh with new seedling in clean system.
Prevention is Easier Than Cure
Root rot causes: Warm water (above 75°F), low dissolved oxygen, high nutrients, poor water circulation. Keep water 65-70°F, ensure air pump runs 24/7, change water every 3-4 weeks.
Algae Growth
Algae isn't necessarily a problem—it's a symptom of a good environment. But heavy algae blocks light from roots and consumes oxygen.
🟢 Algae (Green Water or Slime)
What's Happening:
Algae thrives in light + nutrients + water. You have all three in hydroponics.
Solutions:
- Block Light: Cover reservoir with opaque material (black plastic, cardboard). Algae can't photosynthesize without light. This alone stops 80% of algae.
- Clean Surfaces: Scrub reservoir walls and tubing. Remove settled algae. Algae spores float everywhere but won't grow if no light hits them.
- Water Changes: Fresh water every 3-4 weeks. Old water has accumulated algae spores.
- Reduce Nutrients: Excess nutrients feed algae. Don't overfeed plants—use recommended EC/PPM ranges.
- UV Sterilizer (Optional): UV sterilizers kill algae ($50-150), but blocking light is cheaper and more effective.
- Don't Use Bleach: Kills algae but also damages beneficial bacteria. Overkill—blocking light works.
💡 Algae vs Beneficial Biofilm
Algae (bad): Green/brown, slimy, thick coating on surfaces. Blocks oxygen, consumes nutrients.
Beneficial Biofilm (good): Thin, brown/white layer on roots and surfaces. Contains beneficial bacteria that protect roots.
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Nutrient Deficiencies
Not all yellow leaves mean disease. Often it's just missing nutrients. Use this quick reference:
| Deficiency | Leaf Symptoms | Quick Fix |
|---|---|---|
| Nitrogen (N) | Bottom leaves yellow, veins stay green | Increase EC by 0.2, or add nitrogen-rich fertilizer |
| Magnesium (Mg) | Mid-canopy yellowing between veins | Add Epsom salt (2 tsp per 5 gallons) |
| Iron (Fe) | Top leaves yellow, veins stay green | Lower pH to 5.8. Add chelated iron |
| Potassium (K) | Leaf edges brown/burnt, weak stems | Increase EC by 0.3, or full water change |
| Calcium (Ca) | Blossom-end rot (black spots on fruit) | Increase calcium. Ensure consistent watering. |
| Phosphorus (P) | Purple/reddish stems, delayed flowering | Use flowering nutrient formula (higher P) |
⚠️ Check pH Before Adding Nutrients
Deficiency symptoms often occur with wrong pH, not actual nutrient shortage. If pH is above 6.5, nutrients lock up. Lower pH to 5.8-6.0 first, wait 3 days, then add nutrients if symptoms persist.
Pest Infestations
Hydroponic systems are less prone to pests than soil gardens, but they still happen.
🐛 Aphids
Signs: Tiny green/black insects on stems, sticky residue on leaves, stunted growth
Fix: Spray with neem oil or insecticidal soap. Spray every 3 days for 2 weeks. Remove heavily infested leaves.
🐛 Spider Mites
Signs: Fine webbing on leaves, speckled yellow dots, stunted growth
Fix: Increase humidity (mites like dry air). Spray with neem oil. Isolate infected plant. Mites reproduce fast—act quickly.
🐛 Whiteflies
Signs: Tiny white insects under leaves, leaf yellowing, sticky residue
Fix: Yellow sticky traps trap adults. Spray neem oil on undersides of leaves where they hide.
Equipment Failures
⚡ Pump Not Running
Signs: No water circulation, roots stay dry, algae blooms
Fix: Check power cord. Check outlet (try another device). Listen for hum. If pump hums but doesn't circulate, it's clogged—clean intake filter. If dead, replace pump. Replacement pumps on Amazon.
⚡ Air Pump Not Working
Signs: No bubbles in water, stagnant reservoir, root rot follows quickly
Fix: Check power and outlet. Check air stone—if clogged, replace it (~$5). If pump is silent and won't turn on, it's dead. Air pumps on Amazon (~$20-40).
⚡ Lights Not Working
Signs: Plants stretch, pale color, slow growth or no growth
Fix: Check power cord and outlet. Check if light is dimmable—increase brightness. If LED is off, it's burnt out (rare, but happens). Replace with new LED grow light.
Prevention Tips (Better Than Fixing Problems)
- Keep Water Cool: Maintain 65-72°F. Warm water = low oxygen = root rot. Use water chiller if room is hot.
- Run Air Pump 24/7: Never turn it off. Roots need constant oxygen.
- Change Water Every 3-4 Weeks: Fresh start prevents nutrient imbalances and algae.
- Test pH & EC Twice Weekly: Catch problems before they escalate.
- Cover Reservoir: Blocks algae light, prevents debris from falling in.
- Clean Equipment Regularly: Algae, bacteria, and salt buildup reduce efficiency.
- Quarantine New Plants: Don't introduce pests to your system. Keep new plants separate for 1-2 weeks.
- Monitor Root Color: Check roots weekly. White = healthy. Brown = problem.
Troubleshooting Toolkit
Stock these supplies to handle most hydroponic problems quickly.
Browse Troubleshooting Supplies on Amazon →