How to take a Water Sample for Microbial Analysis

Drinking Water Analysis


Drinking water can contain a wide range of chemical and biological contaminants, including harmful salts, heavy metals, fluorides and feacal coliform bacteria. Using the water analysis results, we can recommend a suitable treatment measure to purify your drinking water. The results are compared against International World Health Organization guide lines for drinking water quality.

How to Collect Drinking Water samples

Water samples for microbial analysis should be collected in sterile bottles, and care should be taken to prevent accidental contamination of the sterile bottle or water sample during sampling and transportation to the water testing laboratory. 

We supply bottles for sampling.  Please email us on to order sample bottles.

Samples should be taken every 6-12 months. Extra samples may be taken if one has done any changes on their drinking water system (e.g changed pipes). Below are procedures for Collecting samples from a tap, river, stream, hand or electric pump, borehole and a well.

Equipment Required

  1. Sterile sample bottles (1 litre)
  2. Water proof marker pen
  3. Sterile gloves
  4. Labeles.

Aseptic collection of a water sample


  1. The technician's hands should be cleaned properly or wear sterile gloves.
  2. The sterile bottle should be held by the base in one hand while the other hand is used to remove the stopper and cover together. 
  3. The stopper and cover should be retained in the hand while the bottle is filled and then they should be replaced together.  
  4. Using a water proof marker fill in the details on the bottle label.

To prevent contamination, the person collecting the water should not touch, or allow any surface to touch the screw thread of the bottle neck or the inside of the cap. If the bottle becomes contaminated, it must not be used. 

Collecting a sample from a tap


  1. Remove any external fittings from the tap, such as anti-splash nozzle or rubber tube.
  2. Clean carefully the outside nozzle of the tap, especially any dirt/grease which has collected. 
  3. Turn the tap on full, and allow the water to run for a while to clear the pipes. This allows time for the nozzle of the tap to be flushed and any stagnant water in the service pipe to bed is charged.
  4. Fill the sample bottle from a gentle flow of water, and replace the cap of the bottle.

Note:Leaking taps may cause contamination of the sample from sources outside the water pipe the therefore leaks should be reported when sampling. A microbiological sample should not be taken until the leak is repaired.

Collecting a sample from a river, stream or other surface water


  1. Aseptically remove the cap and cover of the sterile sample bottle.
  2. Face the mouth of the bottle upstream.
  3. Plunge the neck downwards about 30 cm below the water surface
  4. Tilt the neck slightly upwards to let it fill completely before carefully replacing the cap and cover.
  5. Where there is no current, push the bottle forward horizontally until it is filled.

Collecting a sample from a hand/electric pump/borehole


  1. Continuously operate the pump for at least 5 minutes, letting the water flush the fittings and pipes.
  2. Aseptically collect a sample of water by allowing the water from the pump to flow directly into the sterile bottle. 
  3. Carefully replace the bottle cap and cover.

Collecting a sample from an open well


If the well is one from which water can be raised only by means of a bucket or can, use a  bottle attached to a weight to collect the sample as follows:

  1. Tie a sterile sample bottle onto a length of rope or strong string. 
  2. Use a stone or weight, and attach the bottle just above the weight.
  3. Remove the cap from the bottle, and lower the bottle into the well to a depth of about 1 meter. 
  4. When no more air bubbles rise to the surface, raise the bottle out of the well and replace the cap.

The quality of any analysis is directly related to how well the sample is collected.

Sample handling and dispatch to lab 


  1. Complete the details of the sample and the test required on the label with water proof marker pen.
  2. Immediately after collection, samples should be placed in an insulated cold box with ice blocks and transported immediately to the laboratory.  

Drinking Water Analysis Packages

Code Analysis Name Description Days
CNWA208 Standard Drinking Water Analysis pH, EC, NO3, NH4, P, K, Ca, Mg, SO4, Cu, Fe, Zn, Mn, Mo, Si, B, Na, Cl, HCO3, Fl, Turbidity, Microbiology - Feacal Coliforms (MPN) & E. Coli 7
CNEMA010 Standard NEMA Drinking Water Analysis pH, TSS, NO3, NH4, NO2, TDS, Fl, Cd, Cu, Zn, As, Pb, Se, Feacal Coliforms (MPN) & E. Coli 10
Heavy Metals Analysis As, B, Cd, Co, Cr, Cu, Hg, Pb, Ni, Se, Zn 5
CNWA200 Basic Drinking Water Analysis pH, EC, NO3, NH4, P, K, Ca, Mg, SO4, Cu, Fe, Zn, Mn, Mo, Si, B, Na, Cl, HCO3, Fl, Turbidity 4
ALWA150 Total Coliform and Feacal E.coli MPN, E. Coli 7
NSWA004 Water Borne Diseases Analysis Total Bacteria Count, Total Coliform Count (MPN), Feacal E.coli, Streptococcus sp., salmonella sp., pseudomonas, Vibrio Cholera. 7
SALPR030 Pesticide Residue in Water GC-MS Screening you can request a list of the pesticides that this screen covers 15
SALPR060 Pesticide Residue in Water GC-MS & LC-MS Screening - you can request a list of the pesticides that this screen covers


For more information please contact us through:

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Location: Mashiara Park, Kaptagat Rd, Loresho, Nairobi, Kenya

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