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CIP cleaners — acidic or alkaline, and when to use each

Aqua Filtration System, Faridabad · 9+ years in water treatment · Updated September 2026

Short answer: Use an acidic cleaner for mineral scale and iron deposits, and an alkaline cleaner for organic matter, biofilm and colloidal fouling. Where both are present, always clean alkaline first — acid applied over organic fouling can set the deposit and make it harder to remove.

ROKLEEN acidic and alkaline membrane cleaner
ROKLEEN acidic and alkaline membrane cleaner

Identifying the fouling first

The symptoms tell you which cleaner you need:

SymptomLikely foulingCleaner
Flow down, pressure up, hard feed waterMineral scaleAcidic
Pressure drop across housing risingBiofilm or organicAlkaline
Reddish or brown depositsIron oxidesAcidic
Slimy feel, sometimes odourBiological growthAlkaline
Gradual decline, poor SDI feedColloidal or siltAlkaline
UncertainMixedAlkaline then acidic

What the acidic cleaner does

It dissolves mineral deposits — calcium carbonate, calcium sulphate and metal oxides — by lowering the pH so those salts return to solution.

Best for:

See our ZeroScale acidic membrane cleaner.

What the alkaline cleaner does

It works differently — rather than dissolving minerals, it lifts and disperses organic matter, biofilm and colloidal particles, using surfactants and chelating agents.

Best for:

See our ZeroScale alkaline membrane cleaner.

Why sequence matters

Always alkaline before acidic when both are needed. Organic material often sits on top of mineral scale. Applying acid first attacks the scale underneath while the organic layer remains, and in some cases acid can coagulate the organic matter into a harder deposit. Clean the organic layer off first, then deal with the scale.

Concentration and pH

Follow the product instructions rather than guessing. Two rules apply regardless:

Monitor pH during circulation. If it drifts significantly, the cleaner is being consumed and may need topping up.

Temperature

Warm solution cleans considerably better than cold — but only up to the membrane temperature limit. Exceeding it damages the membrane permanently, so check the datasheet before heating.

The cleaning procedure

The full step by step method is in our CIP cleaning guide. The essentials are:

  1. Record readings before cleaning
  2. Flush with permeate
  3. Circulate at low pressure and higher flow
  4. Soak for 30 to 60 minutes — this does much of the work
  5. Circulate again
  6. Flush thoroughly
  7. Record readings and compare

Safety

Both cleaner types are hazardous.
  • Gloves, eye protection and apron every time
  • Add chemical to water, never water to chemical
  • Never mix acidic and alkaline cleaners — flush thoroughly between stages
  • Store them separately and label clearly
  • Ensure ventilation and have clean water available

What to do between stages

When running both cleaners, flush completely with permeate between them until the pH returns to neutral. Residual alkaline meeting fresh acid produces heat and neutralises both, wasting the chemical and achieving nothing.

If cleaning does not work

ResultWhat it means
Little improvementWrong cleaner chosen, or fouling too advanced
Flow improved, rejection notMembrane ageing alongside fouling
Rejection worse after cleaningPossible pH or temperature damage
Improves then declines quicklyThe underlying cause is still present

That last case is the important one — if performance falls again within weeks, the problem is upstream. Check antiscalant dosing, pre-filtration and recovery. See our membrane life guide.

Preventing the need

Frequent cleaning is a symptom. On a well run plant CIP should be needed once or twice a year. If you are cleaning quarterly, fixing the upstream cause will save both chemical and membrane life.

Need CIP chemicals?

Describe the symptoms and your feed water, and we will recommend the correct cleaner and sequence.

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Frequently asked questions

When should I use an acidic cleaner rather than alkaline?

Acidic for mineral scale and iron deposits, where flow has fallen and pressure risen on hard feed water. Alkaline for organic matter, biofilm and colloidal fouling, which typically shows as rising pressure drop across the housing.

Why must alkaline cleaning come before acidic?

Organic material often sits on top of mineral scale. Applying acid first attacks the scale underneath while the organic layer remains, and acid can coagulate organic matter into a harder deposit.

What water should cleaning solution be mixed with?

Permeate water, never raw water. Mixing with raw water introduces the very salts you are trying to remove, which reduces the effectiveness of the cleaning.

Can acidic and alkaline cleaners be mixed?

Never. They neutralise each other and generate heat. When running both stages, flush completely with permeate between them until the pH returns to neutral.

What if cleaning improves performance but it declines again quickly?

The underlying cause is still present. Check antiscalant dosing, pre-filtration and recovery settings. Frequent cleaning is a symptom of an upstream problem rather than a solution in itself.