"Flushed with chlorine between cycles — system is clean." Three weeks into the new cycle: slime again, root rot again, no idea where it's coming from again.
Pipeline sanitation is not a single procedure once per season. It is two separate tasks with different approaches: removing mature biofilm between cycles, and maintaining cleanliness during active growing.
Quick Glossary
- Biofilm — a colony of microorganisms embedded in a protective polysaccharide matrix on pipe and equipment surfaces
- Hydroponic pipework — all surfaces in contact with solution: pipes, channels, reservoirs, tubing, fittings, pumps, and filters
Between Cycles: How to Clean the System Properly
Between cycles there is time and opportunity to stop the system — this is the best moment for full sanitation. Sequence matters: mechanical cleaning always comes before chemical treatment.
Step 1 — Drain the solution and rinse with water. Remove residual solution and organic matter. Do not skip this step even if the solution "looks normal" — organic deposits on walls are not always visible.
Step 2 — Mechanical cleaning of accessible surfaces. Brushes, pipe cleaners, and sponges for the internal surfaces of reservoirs and channels. The goal is to physically break up and remove the biofilm matrix. Without this step, chemistry only treats the surface layer while inner layers remain intact.
Step 3 — Circulate disinfectant. Fill the system with a working disinfectant solution and run it through all pipes and channels. Options: H₂O₂ at 3–5% concentration, contact time 30–60 minutes. Or PAA at 0.1–0.2%, contact time 20–30 minutes. Chlorine is an alternative — but it is less effective at breaking down organic matrix and leaves organochlorine compounds on surfaces.
Step 4 — Flush with clean water. After the disinfectant, run clean water until EC and odour return to neutral. H₂O₂ and PAA decompose on their own, but flushing accelerates the process and removes reaction residues.
Step 5 — Check before restart. Before introducing new plants, check the pH and EC of the rinse water coming out. If EC is elevated — residual organics or disinfectant are still present; flush again.
During Growing: Maintenance Without Stopping the System
Stopping the system during active growing is not possible — but that does not mean accepting progressively worsening biofilm until the next cycle. Several methods work without harming plants.
Preventive H₂O₂ doses. Low concentrations of hydrogen peroxide — 0.01–0.03% (100–300 mL of 3% H₂O₂ per 100 L of solution) — are safe for plants and effective against early-stage biofilms. Add once every 5–7 days. Higher doses carry a risk of root damage.
Controlling organic load. Regular full or partial solution replacement (25–50% once per week) reduces the organic matter feeding biofilms. Less nutrition — slower colony growth.
UV-C on the recirculation line. UV-C radiation destroys free-floating microorganisms before they can attach to surfaces. It does not remove existing biofilms — but significantly slows their formation in recirculating systems.
Maintaining ORP. When solution ORP stays above 600–650 mV, biofilm development slows. Aeration, small doses of oxidisers, or UV-C help maintain ORP at the required level.
Three Mistakes That Cost the Most
Skipping mechanical cleaning and going straight to disinfectant. Chemistry on a mature biofilm is a waste of time and money. The matrix protects inner layers from disinfectant. Without physically removing the matrix, you are only disinfecting the surface — and the colony recovers within a week.
Applying shock doses of chlorine during growing. Chlorine at concentrations sufficient to destroy biofilm damages roots and eliminates beneficial microflora. For prevention during growing — only mild oxidisers at low doses.
Cleaning only the visible parts of the system. The channel is flushed, the reservoir is scrubbed — but the tubing, fittings, and pump internals are left. These are precisely the places where flow is slowest and surfaces are most convoluted — ideal conditions for biofilm. Full sanitation means circulating disinfectant through every section of the system, including dead-end branches.
How to Know Sanitation Worked
- Rinse water coming out has a neutral odour and EC close to source water EC
- Reservoir and channel walls feel smooth with no sticky deposits when checked by hand
- New cycle starts without characteristic solution odour during the first two weeks
- If odour appears in the first week of a new cycle — sanitation was incomplete or hidden biofilm zones remain in the system