After the first harvest, most beginners drain the reservoir, wipe it with a paper towel, and re-plant. Six weeks later they wonder why germination is patchy and roots look brown. The culprit is almost always biofilm — a slimy microbial layer that clings to reservoir walls, pump housings, and net cups.
What you'll need
- 3% household hydrogen peroxide (or unscented bleach at 1:10)
- An old toothbrush and a bottle brush
- Warm tap water
- Clean microfibre cloth
The 30-minute routine
- Unplug and drain. Tip the reservoir into the sink; do not pour spent nutrient onto houseplants — the salt load is too high.
- Disassemble. Remove the pump, air stone, net cups, and light hood if it lifts off.
- Soak. Fill the reservoir with warm water and 250 ml of 3% peroxide. Drop the pump and net cups in.
- Scrub. Work the toothbrush around pump impellers and net cup ribs — that's where biofilm hides.
- Rinse twice. Peroxide residue can shock young roots. Two full rinses is the safe minimum.
- Air-dry 10 minutes. Reassemble only when everything is bone-dry.
Never lose a second-cycle grow to biofilm again
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How often?
Between every grow at minimum. If you're running lettuce back-to-back for months, do a mid-cycle wipe-down of the water line every 3 weeks — that's where algae takes hold first.
Related: 10 Common Hydroponic Mistakes · Hydroponic Water Quality · pH and EC for Beginners · Hydroponics for Beginners
Frequently asked questions
Can I use vinegar instead of peroxide?
Vinegar dissolves mineral scale but doesn't kill biofilm well. Use vinegar for a quarterly descaling and peroxide for the between-grow sanitize.
Do I need to clean if the water still looks clear?
Yes. Biofilm is transparent until it's thick. Clear water with slimy walls is the classic setup for root rot in cycle two.
Is bleach safe for hydroponic gear?
At 1:10 dilution with a thorough double-rinse, yes. Never mix bleach with peroxide or vinegar.
How do you clean a hydroponic system between grows?
Drain the reservoir, disassemble the pump and net cups, soak everything in warm water with 250 ml of 3% hydrogen peroxide, scrub biofilm off with a toothbrush, rinse twice, and air-dry before reassembly. The full routine takes about 30 minutes.
How often should you clean a hydroponic reservoir?
Do a full sanitize between every grow cycle. For back-to-back lettuce or basil runs, wipe the water line every 3 weeks — that is where algae takes hold first.
What kills biofilm in a hydroponic system?
3% hydrogen peroxide at roughly 250 ml per 4 L of warm water. Bleach at 1:10 works too but needs a thorough double-rinse. Vinegar does not reliably kill biofilm on its own.
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