What causes root rot in hydroponics?

Root rot is most often caused by Pythium (a water mould), water temperatures above 22°C, insufficient oxygen in the reservoir, or light leaking into the reservoir and encouraging algae growth. Symptoms include brown or slimy roots, a foul smell from the reservoir, and wilting despite adequate water.

How do you fix root rot in a hydroponic system?

Add a larger air stone and increase air pump size, reduce reservoir temperature to 18–20°C, and use a beneficial bacteria product such as Hydroguard or SM-90. Block all light from reaching the reservoir. In severe cases, flush the system, prune affected roots, and sterilise the reservoir.

Why are my hydroponic plant's leaves turning yellow?

Yellowing that starts on older, lower leaves usually points to nitrogen deficiency; yellowing between the veins while the veins stay green points to iron or magnesium deficiency. pH outside the 5.5–6.5 range is often the real cause, since it blocks nutrient uptake — check and correct pH before treating it as a straightforward deficiency.

What is nutrient lockout and how do I fix it?

Nutrient lockout is when plants show deficiency symptoms even though nutrients are present in the solution, usually because pH is outside the absorption range or EC is too high. Fix it by correcting pH to 5.8–6.2, flushing with plain pH-adjusted water for 24–48 hours, and rebuilding nutrient concentration gradually.

Why does my hydroponic reservoir's pH keep drifting?

pH drift is usually caused by microbial activity in the reservoir, plant nutrient uptake unbalancing the solution, insufficient buffering, or high-alkalinity tap water. Check pH at the same time each day, keep the reservoir sealed to limit CO₂ off-gassing, use a pH-buffered nutrient formula, and consider RO water if tap alkalinity is high.

How do I get rid of pests in a hydroponic system?

Inspect plants weekly, especially the undersides of leaves. For fungus gnats, let media dry slightly between waterings and use sticky traps; for spider mites, use a neem oil spray and increase humidity. Quarantine all new plants before introducing them to your grow room, and keep the area clean since debris attracts pests.

What causes calcium deficiency in hydroponics?

Calcium deficiency is usually caused by pH below 5.5 locking out calcium, insufficient CalMag supplementation (especially with soft or RO water), poor airflow (calcium uptake is driven by transpiration), or excess potassium/magnesium competing for uptake. It shows up as tip burn on young leaves or blossom end rot on tomatoes and peppers.

What should I check first when something goes wrong in hydroponics?

Always check pH first — more than half of hydroponic problems trace back to pH drift. The order is: check pH, then EC, then inspect the roots, then check the environment (temperature, humidity, airflow).

Troubleshooting

Hydroponic Troubleshooting Guide: Diagnose & Fix Common Problems

By HiGroPonics Team · Updated June 2026

Every grower faces problems. The difference between an experienced grower and a beginner isn't that the experienced grower has fewer problems — it's that they can identify and resolve them faster.

This guide covers the most common issues, their symptoms, likely causes, and how to fix them. When in doubt, always check pH first — more than half of all hydroponic problems trace back to pH drift.

First rule of troubleshooting

Check pH → Check EC → Check roots → Check environment. In that order.

Common Issues

Diagnose Your Problem

🟡

Yellowing Leaves (Chlorosis)

Symptoms

▸Leaves turning yellow, starting with older (lower) growth
▸Yellowing between veins while veins stay green
▸Uniform pale yellow across the whole plant

Likely Causes

▸Nitrogen deficiency (most common)
▸Iron or magnesium deficiency
▸pH out of range — blocking nutrient uptake
▸Overwatering / root suffocation

How to Fix

✓Check and correct pH to 5.5–6.5 first
✓Test EC — if low, increase nutrient strength gradually
✓Check roots for signs of rot (brown, slimy)
✓If veins stay green, suspect iron deficiency — pH likely too high

🟤

Root Rot

Symptoms

▸Roots are brown or tan instead of white
▸Roots feel slimy or mushy
▸Foul smell from the reservoir
▸Plant wilting despite adequate water

Likely Causes

▸Pythium (water mould) — most common cause
▸Water temperature too high (above 22°C)
▸Insufficient oxygen in the reservoir
▸Light leaking into the reservoir (algae growth)

How to Fix

✓Add a large air stone and increase air pump size
✓Reduce reservoir temperature — aim for 18–20°C
✓Use a beneficial bacteria product (Hydroguard, SM-90)
✓Block all light from reaching the reservoir
✓In severe cases: flush system, prune affected roots, sterilise reservoir

🔒

Nutrient Lockout

Symptoms

▸Plants look deficient despite nutrients being present
▸Multiple deficiency symptoms at once
▸Leaves browning at tips or edges
▸Stunted growth even with correct EC

Likely Causes

▸pH outside the absorption range (most common)
▸Nutrient solution too concentrated (EC too high)
▸Antagonism between nutrients (e.g. excess calcium blocking magnesium)
▸Salt buildup in growing media

How to Fix

✓Correct pH to 5.8–6.2 and monitor daily for drift
✓Flush with plain pH-adjusted water for 24–48 hours
✓Reduce nutrient concentration and rebuild gradually
✓Check individual nutrient ratios — CalMag deficiency is common

📉

pH Drift

Symptoms

▸pH reading shifts significantly between checks
▸Plants show different deficiency symptoms each time
▸pH rises or falls consistently in one direction

Likely Causes

▸Microbial activity in reservoir (pH rise)
▸Plant uptake unbalancing the solution
▸Insufficient buffering in the nutrient solution
▸Tap water with high alkalinity (causes upward drift)

How to Fix

✓Check pH at the same time each day and adjust as needed
✓Ensure reservoir is sealed to limit CO₂ off-gassing
✓Use a quality pH-buffered nutrient formula
✓Consider RO water if tap water alkalinity is very high
✓Change reservoir solution weekly if drift is severe

🐛

Pests

Symptoms

▸Tiny insects on leaves or in growing media
▸Sticky residue (honeydew) on leaves
▸Speckled, curled, or distorted leaves
▸Fine webbing on leaf undersides (spider mites)

Likely Causes

▸Fungus gnats — larvae in media, attracted by moisture
▸Spider mites — spread via contaminated cuttings or open windows
▸Aphids — often arrive on new plants or clones
▸Thrips — tiny fast-moving insects, leave silvery trails

How to Fix

✓Inspect plants weekly, especially leaf undersides
✓For fungus gnats: allow media to dry slightly between waterings, use sticky traps
✓For spider mites: neem oil spray, increase humidity
✓Quarantine all new plants before introducing to your grow room
✓Keep grow room clean — debris and dead leaves attract pests

💨

Mould & Mildew

Symptoms

▸White powdery coating on leaf surfaces (powdery mildew)
▸Grey or brown fuzzy patches on plant matter (botrytis)
▸Dark patches spreading across leaves or stems

Likely Causes

▸Humidity too high — above 70% in late vegetative / flowering
▸Poor air circulation
▸Overcrowding — plants touching each other
▸Water sitting on leaves (avoid overhead watering)

How to Fix

✓Improve airflow — add a second circulation fan
✓Keep humidity 40–60% for most crops (lower for flowering)
✓Remove and dispose of affected plant material immediately
✓Prune lower leaves to improve airflow through the canopy
✓For powdery mildew: diluted potassium bicarbonate spray

🌡️

Heat Stress

Symptoms

▸Leaf edges curling upward (taco-ing)
▸Wilting during the day even with adequate water
▸Bleaching or whitening near the light source
▸Stunted growth, reduced yield

Likely Causes

▸Air temperature above 28°C at canopy level
▸Lights too close to plants
▸Insufficient extraction — warm air building up
▸Reservoir temperature above 22°C (affects root zone)

How to Fix

✓Check canopy temperature — target 22–26°C
✓Increase fan speed or add an additional extraction unit
✓Raise lights or reduce intensity during peak heat
✓Cool the reservoir with a small aquarium chiller if needed
✓Use a climate controller to automate extraction based on temperature

Nutrient Issues

Deficiencies & Toxicity

Always correct pH before treating any deficiency — most nutrient problems are lockout caused by pH drift, not a genuine shortage.

🔥

Nutrient Burn (EC Too High)

Symptoms

▸Brown or crispy tips and edges, starting on newer growth
▸Leaf tips curl downward
▸Overall dark, almost unnaturally green colour before browning begins
▸In severe cases, whole leaves brown and die

Likely Causes

▸EC too high for the crop or growth stage
▸Added too much nutrient concentrate
▸Plants drinking water faster than nutrients — EC rises as reservoir level drops without topping up
▸Switched to a stronger formula too quickly

How to Fix

✓Check EC and compare to target range for your crop and stage
✓Dilute reservoir with plain pH-adjusted water
✓Top up daily with plain water (not nutrient mix) when level drops
✓Rebuild EC gradually — increase by no more than 0.2–0.3 mS/cm per day

🌿

Nitrogen Deficiency

Symptoms

▸Yellowing starting on the lowest, oldest leaves and progressing upward
▸Uniform pale green to yellow — whole leaf, not between veins
▸Slow growth, small leaves, reduced vigour
▸Stems may redden in some crops (tomatoes, peppers)

Likely Causes

▸EC too low — solution is too dilute
▸Using a bloom (low-N) formula during vegetative growth
▸pH too high (above 6.8) partially locking out nitrogen
▸Reservoir solution old and nutrient-depleted

How to Fix

✓Check EC — increase nutrient strength gradually if below target
✓Confirm you are using a veg/grow formula (high N) during vegetative stage
✓Correct pH to 5.8–6.5
✓Replace reservoir solution if it is more than 1–2 weeks old

🥬

Calcium Deficiency

Symptoms

▸Tip burn on inner and younger leaves — common in lettuce and leafy greens
▸Blossom end rot on tomatoes and peppers (dark, sunken patch at fruit base)
▸Distorted, curled, or stunted new growth
▸Brown spots or dead patches on young leaves

Likely Causes

▸pH below 5.5 locking out calcium
▸Insufficient CalMag supplementation, especially with soft or RO water
▸Poor airflow — calcium uptake is driven by transpiration
▸Excess potassium or magnesium antagonising calcium uptake

How to Fix

✓Raise pH above 5.5
✓Add a CalMag supplement
✓Improve canopy airflow with a circulation fan
✓If using RO water, use a calcium-fortified base formula

🍂

Magnesium Deficiency

Symptoms

▸Interveinal chlorosis on older, lower leaves — veins remain green while tissue between turns yellow
▸Symptoms appear on mature growth first and progress upward over time
▸Leaf edges may redden or brown in later stages
▸Often confused with iron deficiency — magnesium affects old growth, iron affects new

Likely Causes

▸pH below 5.5 or above 7.0
▸Excess calcium or potassium antagonising magnesium uptake
▸Low EC or depleted nutrient solution
▸Not using a CalMag supplement with soft water or coco coir

How to Fix

✓Correct pH to 5.5–6.5
✓Add Epsom salts (magnesium sulphate) at 1–2 g per litre
✓Add or increase CalMag supplement
✓Check that calcium levels are not excessively high

💛

Iron Deficiency

Symptoms

▸Interveinal chlorosis on the youngest, newest leaves — veins stay green, tissue between turns yellow
▸New growth appears pale green or almost white in severe cases
▸Older leaves remain unaffected initially — opposite pattern to magnesium deficiency
▸Most common micronutrient deficiency in hydroponics

Likely Causes

▸pH above 6.5 — iron precipitates out of solution (most common cause)
▸Non-chelated iron in low-quality nutrient formulas
▸Cold reservoir temperatures slow iron uptake
▸Excess phosphorus or manganese competing with iron uptake

How to Fix

✓Reduce pH to 5.5–6.2 — iron becomes available again quickly
✓Add a chelated iron supplement (e.g. Fe-EDTA or Fe-DTPA) if correction is slow
✓Ensure reservoir temperature is above 18°C
✓Use a complete base nutrient with chelated micronutrients

💧

Overwatering / Waterlogging (Media Systems)

Symptoms

▸Yellowing and wilting despite correct pH and EC
▸Media feels permanently wet and never dries between feeds
▸Roots look pale or brown but without the slime associated with Pythium
▸Slow, stunted growth in an otherwise healthy-looking system

Likely Causes

▸Drip or flood timer set to water too frequently
▸Coco coir compacted or used without perlite — poor internal drainage
▸Drainage holes blocked or too small
▸Container too large for plant size — roots cannot dry the media evenly

How to Fix

✓Reduce watering frequency — coco should approach (but not reach) dryness between feeds
✓Mix perlite into coco at a 70:30 ratio to improve drainage and aeration
✓Check all drainage holes are clear and unobstructed
✓Match container size to plant size — oversized containers stay wet too long

🔄

When to Cut Your Losses

Sometimes the right decision is to end a grow, sterilise your system, and start fresh. This is the correct call when: root rot has spread to more than 50% of the root zone, powdery mildew is systemic across multiple plants, or your nutrient solution has been contaminated beyond recovery.

A failed grow is not wasted time — it is the fastest route to understanding your system. Document what happened, clean thoroughly with a dilute hydrogen peroxide solution, and apply what you learned.

FAQ

Frequently Asked Questions

What causes root rot in hydroponics?: Root rot is most often caused by Pythium (a water mould), water temperatures above 22°C, insufficient oxygen in the reservoir, or light leaking into the reservoir and encouraging algae growth. Symptoms include brown or slimy roots, a foul smell from the reservoir, and wilting despite adequate water.
How do you fix root rot in a hydroponic system?: Add a larger air stone and increase air pump size, reduce reservoir temperature to 18–20°C, and use a beneficial bacteria product such as Hydroguard or SM-90. Block all light from reaching the reservoir. In severe cases, flush the system, prune affected roots, and sterilise the reservoir.
Why are my hydroponic plant's leaves turning yellow?: Yellowing that starts on older, lower leaves usually points to nitrogen deficiency; yellowing between the veins while the veins stay green points to iron or magnesium deficiency. pH outside the 5.5–6.5 range is often the real cause, since it blocks nutrient uptake — check and correct pH before treating it as a straightforward deficiency.
What is nutrient lockout and how do I fix it?: Nutrient lockout is when plants show deficiency symptoms even though nutrients are present in the solution, usually because pH is outside the absorption range or EC is too high. Fix it by correcting pH to 5.8–6.2, flushing with plain pH-adjusted water for 24–48 hours, and rebuilding nutrient concentration gradually.
Why does my hydroponic reservoir's pH keep drifting?: pH drift is usually caused by microbial activity in the reservoir, plant nutrient uptake unbalancing the solution, insufficient buffering, or high-alkalinity tap water. Check pH at the same time each day, keep the reservoir sealed to limit CO₂ off-gassing, use a pH-buffered nutrient formula, and consider RO water if tap alkalinity is high.
How do I get rid of pests in a hydroponic system?: Inspect plants weekly, especially the undersides of leaves. For fungus gnats, let media dry slightly between waterings and use sticky traps; for spider mites, use a neem oil spray and increase humidity. Quarantine all new plants before introducing them to your grow room, and keep the area clean since debris attracts pests.
What causes calcium deficiency in hydroponics?: Calcium deficiency is usually caused by pH below 5.5 locking out calcium, insufficient CalMag supplementation (especially with soft or RO water), poor airflow (calcium uptake is driven by transpiration), or excess potassium/magnesium competing for uptake. It shows up as tip burn on young leaves or blossom end rot on tomatoes and peppers.
What should I check first when something goes wrong in hydroponics?: Always check pH first — more than half of hydroponic problems trace back to pH drift. The order is: check pH, then EC, then inspect the roots, then check the environment (temperature, humidity, airflow).

Dig Deeper

Understanding pH & EC →Nutrient Mix Calculator →Glossary of Terms →

Ready to set up your grow? Open the System Builder → for a checklist of what you need, indicative prices, and links to find everything.