Found slime in the pipes — flushed with chlorine — two weeks later the slime is back. Sound familiar? The problem is not that you used too little chlorine. The problem is that chlorine kills free-floating bacteria but does not destroy the biofilm itself. A biofilm is not "dirt" you can wash away. It is an organised colony of microorganisms inside a protective matrix — deliberately constructed to survive rinsing, chlorination, and most standard disinfection methods.
Quick glossary: Biofilm — an organised community of microorganisms (bacteria, fungi, protozoa) attached to a surface and protected by a polysaccharide matrix; tens of times more resistant to disinfectants than the same microorganisms in free suspension. Slime in pipes and channels — the visible sign of a mature biofilm, but the biofilm itself forms long before any slime becomes visible. Sanitation in hydroponics — a system of regular preventive measures that stops biofilm accumulation, not a one-off reaction to its appearance.
How Biofilms Form and Why They Are Hard to Eliminate
Biofilm formation is a staged process. Individual bacteria first attach to the surface of a pipe, channel, or root. They then begin secreting a polysaccharide matrix — the "cement" that holds the colony together and shields it from the outside environment. In a mature biofilm there are channels for nutrient circulation and zones with different conditions: aerobic on the outside and anaerobic at the core.
That anaerobic core is the source of pathogens. Pythium, Fusarium, and bacterial pathogens survive and multiply in these protected zones even when external conditions appear normal. When a fragment of the biofilm breaks off and reaches the root — infection begins.
Chlorine and most standard disinfectants are effective against free-floating microorganisms but penetrate the biofilm matrix poorly. A single shock dose of chlorine destroys the surface layer — but within a week the colony recovers from the cells that survived deep inside.
Where Biofilms Form First
Not all parts of the system are equally vulnerable. Biofilms form where three conditions combine: a surface, a food source, and a relatively stable environment.
Dead zones with low flow — channel corners, pipe joints, check valves, filters. Flow is slower there, organics settle, and bacteria have time to attach.
The root zone — the root itself releases exudates that serve as food for microorganisms. Without sufficient DO, anaerobic zones form directly between the roots.
Inner surfaces of dark reservoirs — darkness and warmth accelerate growth. Transparent reservoirs are easier to inspect visually, but they must be shaded to avoid stimulating algae growth.
How to Control Biofilms Systematically
Biofilm control is prevention, not reaction. By the time slime is visible, the biofilm is already mature and requires mechanical removal — not just chemistry.
Mechanical cleaning between cycles — the only reliable way to remove a mature biofilm. Brushes, pipe cleaners, pressure washing. Chemical treatment after mechanical cleaning is for surface disinfection — not for removing the matrix.
Regular preventive use of oxidisers — H₂O₂ (hydrogen peroxide) or PAA (peracetic acid) in low doses between cycles or once a week during active growing. They break down the biofilm matrix more effectively than chlorine and decompose quickly in solution.
ORP monitoring — ORP reflects the solution's capacity to oxidise and disinfect. Above 650–700 mV, the development of pathogens and biofilms slows substantially. ORP can be maintained through aeration, oxidisers, or UV-C.
Organic load management — the more organics in the solution (fertiliser residues, root debris, dead cells), the faster biofilms grow. Regular full or partial solution changes reduce this load.
Three Mistakes That Cost the Most
Flushing the system with chlorine without mechanical cleaning and assuming it is now disinfected. Chlorine eliminates free bacteria but not the matrix. The next cycle, the biofilm recovers from the cells that survived deep inside. Mechanical cleaning is the mandatory first step; chemistry comes second.
Starting a new cycle without full sanitation of the reservoir and pipes after Root Rot. The pathogens that caused Root Rot live in the biofilm on the system walls. Simply draining and refilling with fresh solution is not enough. The new cycle starts already infected.
Skipping dead zones during cleaning. You cleaned the channel and the reservoir — but the corners, joints, and hoses were left. That is exactly where flow is slowest and the most resistant biofilms grow. Complete sanitation means every surface that contacts the solution.
How to Know Biofilms Are Under Control
After cleaning and between cycles: no visible slime, reservoir walls and pipes feel smooth without any sticky coating, solution smell is neutral or mildly plant-like — no sour, putrid, or "swampy" odour. Solution ORP is consistently above 600 mV. If a smell appears before visible slime — a biofilm is already present, just not yet mature.
For deeper understanding: Pipeline Sanitation: Removing Organic Build-up Without Stopping the System — specific cleaning protocols for a live running system.