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Alabama Agricultural Irrigation Information Network

Chlorination to Prevent Clogging

Steven P. Kovach, Extension Horticulturist

Larry M. Curtis, Extension Agricultural Engineer

James E. Hairston, Extension Water Quality Scientist

Irrigating with a micro-system offers improved crop quality and yield with significant savings of energy and water. Achieving these benefits consistently requires an effective water treatment program to prevent clogging, the most common problem of micro-irrigation. This publication explains what you need to know about chlorination to prevent clogging and gives an easy, step-by-step procedure to help you do the job right.

Chlorination-The What And The Why

  • Injected into your micro-inigation system, chlorine kills the micro-organisms-bacteria, fungi and algae-that may be in your water source and are the most common system cloggers. Usually, chlorinating at moderate injection levels once a week will keep lines and emitters clear of clogging by micro-organisms.
  • Chlorine is most readily available as household liquid bleach, which is usually a 5.25% solution. (Econo-type bleaches may have less chlorine-read the label.) Irrigation system suppliers may offer solutions of up to 15% at less cost in higher quantities. The dry powder chlorine used in swimming pools may react with minerals to actually cause clogging. Gaseous chlorine is least expensive, but can be extremely hazardous and requires special equipment and training of workers.
  • Chlorine decomposes readily in sunlight or when exposed to heat or air, and so must be stored and handled carefully. Chlorine is also corrosive to most metals. The ideal container or injection supply tank is white, opaque plastic with a secure lid or other closure, placed in a shaded location. Avoid placing black containers in the sun. Do not allow containers to remain open to the air for more than a few minutes.
  • Chlorine must be injected upstream of the system filters, to catch any solid particles that may result from chlorine reacting with impurities in the water, and to allow the filters to trap micro-organisnis killed in the treatment process. Never inject chlorine at the same time with fertilizers, since their chemical reaction will almost certainly cause problems.
  • Water quality is very important-some kinds of water quality problems can make chlorination ineffective or even cause clogging as a result of chlorination. Check ANR-649 in this handbook for details. Water pH is critical and must be checked each time chlorination is done to be sure it is under 7.5. If your water pH is above 7.5, your county Extension agent can help you get a more complete water analysis. If your water source is a pond or lake, check pH and plan on chlorinating early in the day, since pH may rise rapidly during the day.
  • Chlorine injected into the system in effect is "used up" (or tied up) in chemical reactions with organic matter and other water impurities. To know for sure whether you have put in enough chlorine to destroy all micro-organisms you must test for free chlorine (not "total chlorine") in the water after injection. That is, if some amount of free chlorine is still available, you know you have put in enough plus a little more. A simple kit is available to make this test.

Chlorination Procedure

Chlorination requires that your system have adequate filtration and that you are able to determine the flow rates of both your system and your injection pump. Knowing these flow rates is very important for successful chlorination. For information on this and other basic chemigation procedures, see Circular ANR-650 in this handbook.

The only equipment needed is a color-wheel type test kit for pH and a D.P.D. type test kit (such as the Hach kit) for free chlorine. The "orthotolodine" type kit used for swimming pools is not adequate.

The END RESULT aimed at is a free chlorine level at the emitter farthest from the injection pump of at least 1.0 part per million (ppm), with this level maintained for at least 30 minutes, the time needed to be sure of killing all micro-organisms. Because the free chlorine level that results after injection can't be exactly predicted, you must actually test the water for free chlorine after injection is started. IMPORTANT: The test required is for free chlorine; a "total chlorine test" shows chlorine that may already be used up or tied up in the water and not available to kill micro-organisms.

Chlorination-Step by Step

The diagram below shows the basic steps involved in chlorination, with more detailed information given below. The procedure as presented is a simplified method designed for typical systems. It is based on using a 90-minute injection period and a desired initial total chlorine concentration of 20 parts per million, and should be adequate for most situations. An alternate method for Steps 3 and 4, explaining calculations for different chlorine concentrations and injection periods, is given on page 5. As you gain experience, you will learn how to make adjustments to fit your changing situation. If your system is divided into zones, you must chlorinate them separately. Since chlorination of the first zone will clean filters and mains, the second zone done on the same day can, if desired, be chlorinated using a lower chlorine concentration.

STEP 1. Test the pH of your water, taking the sample from the discharge side of the pump, to be sure it is under 7.5. Because pH varies, especially in slow flowing surface water sources (pond or lake), you should do this before every chlorination.

STEP 2. with the system operating at normal pressure and flow rate, back-flush the filters. This adds to the effectiveness of chlorination. Allow system to return to normal operating pressure and flow.

STEP 3. Determine the amount of liquid chlorine solution (5.25% bleach) to use for the 90-minute injection period. This amount depends on the system flow rate, as read from the system flow meter (design specifications are not accurate enough). The formula to obtain an initial 20 ppm total chlorine concentration is:

                      Chlorine amount = 0.0343 x system flow rate

                          (gal/1 .5 hr)                     (gal/min)

Example: If system flow rate is 35 gal/min, amount of chlorine solution to use is 1.2 gallons:

Chlorine amount = .0343   x   35 gal/min = 1.2 gal

Convert the tenths into ounces by multiplying times 128:

0.2 x 128 = 26 ounces. Amount of chlorine solution

= 1 gallon 26 ounces.

NOTE:If you are using a 10% chlorine solution, use half the amount calculated. For a 15% solution, use one-third the amount.

The table below shows amounts of 5.25% chlorine solution to use for several common system pump flow rates.

STEP 4. Turn on your injection pump and measure its flow rate. Checking and calibrating the injection pump each time you chlorinate is a good idea because injection pumps may vary and you need an accurate idea of the actual injection rate each time.

Find out the total water + chlorine amount to be injected simply by multiplying the injection pump flow rate by 1.5. Then subtract the chlorine amount (Step 3) to find the amount of water needed.

Example: If the injection pump flow rate is 10 galft, water + chlorine amount needed is:

10 gal/hr  x  1.5 hr = 15 gal

If the chlorine amount needed (Step 3) is 1.2 gallons, then 15 - 1.2 = 13.8 gallons of water needed.

The table below shows water + chlorine amounts for several common injection rates.

 STEP 5. Start the injection pump, wait several minutes (for chlorine solution to pass the filters) then take a water sample downstream (after the filters) and use the D.P.D. test kit to check free chlorine. This reading should be at or near 3.0 ppm.

  • If the reading is at 3.0, go to Step 6.
  • If the reading is above 3.0, turn the injection pump rate down slightly, wait 3 minutes, then recheck the chlorine level. Repeat this step until the reading stays at or near 3.0.
  • If the reading remains well below 3.0 and you backflushed the filters before beginning chlorination, you may have unforeseen water quality problems and should call your County Extension Agent for assistance in getting a more complete water quality test.

CAUTION: Take the D.P.D. test reading within 15 seconds after adding the reagent chemical. After doing the test, rinse the test tube thoroughly with fresh water (not system water) to be sure it is free of chlorine residues.

STEP 6. After the chlorine has had time to reach the farthest emitter, test for free chlorine at that point. The reading should be at least 1.0 ppm. If it is below 1.0 re-check at five-minute intervals. When the reading reaches 1.0, note the time. You can stop injection after 30 minutes from that time.

If you cannot get a free chlorine reading with at least 30 minutes of injection time left (and you had at least a 3.0 reading after the filter) your lines probably have a great deal of organic matter in them, and you should repeat the entire chlorination process to this point.

STEP 7. After chlorination is completed, shut down the system with chlorine still in the fines. On the following day, restart the pump and flush the entire system beginning with the main, submain, and zone manifold. Finally, flush one lateral at a time until water runs clear. The reason for flushing one lateral at a time is to assure enough pressure to thoroughly flush each lateral.

NOTE: Any chlorine solution left in the injection supply container should be dumped. Mix a new batch just before each chlorination. if you need to reduce the amount being injected, remember to reduce both the chlorine and the dilution water amounts proportionally.

Example: In a 9-gallon injection amount containing 3 gallons of 5.25% chlorine + 6 gallons water, the proportion is 3 parts chlorine to 6 parts water, or 1:2. To reduce the 9-gallon amount by 1.5 gallons, reduce the chlorine by 0.5 gallon (1 part) and the water by 1.0 gallon (2 parts).

   STEP 3                                                                           STEP 4

Amount of 5.25% Chlorine Solution to Use                Amount of Water + Chlorine to Use

(For 90-min injection period, 20 ppm total           (For 90-min injection period, 20 ppm total

chlorine concentration)                            chlorine concentration)

System flow rate


Chlorine amount


Injection Pump Rate


Water + Chlorine



1.54(1 gal + 4 3/8 pt)





1.71(1gal + 5 3/4 pt)




1.89(1gal + 7 1/8 pt)




2.06(2 gal + 1/2 pt)




2.23(2 gal + 1 7/8 pt)




2.4(2 gal + 3 1/4 pt)




2.57 (2 gal + 4 5/8 py)




2.74(2 gal + 6 pt)




2.91(2 gal +7 3/8 pt)




3.09(3 gal + 3/4 pt)




3.26(3 gal + 2 1/8 pt)




3.43(3 gal + 3 1/2 pt)



Each gal/min of flow rate= 4.4 oz of 5.25% chlorine                           Multiply injection pump rate by 1.5 to find

to be injected.                                                                                           water + chlorine amount.

How Often Should a Micro-System Be Chlorinated and Flushed?

As a general rule, systems using surface water sources should be chlorinated once a week. Systems using well water should be chlorinated every two weeks. These intervals may be lengthened to not more than once a month if the system is known to be clean and functioning at design specifications at the outset and close monitoring of system flow rate with an accurate, propeller-type flow meter shows no drop in flow rate during the interval.

If chlorination is done at least every two weeks and followed by thorough flushing, no additional flushing is needed. If the chlorination interval is lengthened to one month, several randomly selected laterals should be flushed at the two-week point to test for sediment build-up. If sediment is detected, the entire system (main, submain, manifolds and laterals) should be flushed every other week. Chlorination will not prevent plugging from sediment.

Close monitoring and observing the recommended chlorination and flushing intervals gives a grower the best chance of avoiding problems, not only of obvious clogging but also loss of application uniformity, which can seriously affect crop yield and quality.

Super-Chlorination-using an injection rate as high as 500 ppm-may clear lines that have become very clogged because the system has not been chlorinated regularly. Super-chlorination is not recommended as a replacement for a regular preventive treatment program. It is, however, part of the routine end-of-season maintenance-see Circular ANR-655 in this handbook. Alternate Steps 3 & 4 of this publication, explain how to chlorinate at any chosen injection rate.

ALTERNATE METHOD FOR STEPS 3 AND 4. If you prefer, you can use the following formulas instead of the simplified method, to adjust for varying system conditions.

ALTERNATE STEP 3. The simplified procedure given in this Circular is based on a desired chlorine concentration after injection of 20 ppm. If pH is below 7.5, water quality is good, and the system has been chlorinated recently, a chlorine concentration as low as 5 ppm might be chosen.

The following formula allows you to adjust for water quality and system condition by choosing an appropriate total chlorine concentration after injection. The formula calculates the chlorine injection rate needed; that is, how many gallons of chlorine solution to inject per hour. Other factors in the formula are system flow rate in gallons per minute and percent strength of chlorine source used.

CIR (gal/hr) Q (gal/min) x C (ppm) x .006/S%


CIR = chlorine injection rate

    Q = system flow rate

    C = desired chlorine concentration

     S = percent strength of chlorine source

Example. If system flow rate Q is 100 gal/min, you choose to inject to obtain a system total chlorine concentration (C) of 10 ppm, and you use a 5.25% chlorine source (S), such as household bleach, then the injection rate CIR is:

CIR = 100 x 10 x 0.006/5.25

        = 100 x 10 x 0.00114

        = 1. 14 gallons chlorine solution/hour.

ALTERNATE STEP 4. Next, determine the total time period needed for injection and the amounts of chlorine solution and water to add to the injection supply tank.

1. The total injection period (IP) needed equals 30 minutes contact time + your system's pass-through time. For example, if after your system reaches normal operating pressure water takes 25 minutes to pass from the pump to the farthest emitter, your IP is 30 + 25 = 55 minutes.

2.To achieve the desired injection time (IP), a certain total amount (TA) of water + chlorine solution must be put in the injection supply tank, based on the injection pump flow rate (IR):

TA (gal) = IR (gal/hr) x IP (hr)

Example: IP is 55 minutes and injection pump flow rate (IR) is 10 gallons per hour. Total water + chlorine solution amount (TA) needed is: 10 gal/hr x 55/60 hr = 9.2 gallons.

3. The part of this total amount made up by chlorine solution depends on the injection period (IP) and the chlorine injection rate (CIR) determined in Step 3. Chlorine solution amount (CA) is:

CA (gal) = IP (hr) x CIR (gal/hr)

Example: If IP is 55 minutes and CIR is 1.14 gal/hr, then amount of chlorine solution to use is 55/60 x 1.14 = 1.05 gallons.

4. The rest of the total amount (TA) is water (WA):

WA (gal) = TA (gal) - CA (gal)

Example: If the total amount needed is 9.2 gallons and chlorine solution amount is 1.05 gallons, water amount to add is 9.2 - 1.05 = 8.2 gallons (approx.).

(For information on determining pass-through time and injection pump flow rate, see Circular ANR-650.)

Publication No.

Micro-Irrigation Handbook ANR-651


Larry M. Curtis, Extension Agricultural Engineer, Professor, Biosystems and Agricultural Engineering, and

Ted W. Tyson, Extension Agricultural Engineer, Associate Professor, Biosystems and Agricultural Engineering,

Steven P. Kovach, Extension Water Quality Scientist

Issued in furtherance of Cooperative Extension work in agriculture and home economics, Acts of May 8 and June 30, 1914, and other related acts, in cooperation with the U.S. Department of Agriculture. The Alabama Cooperative Extension System (Alabama A&M University and Auburn University) offers educational programs, materials, and equal opportunity employment to all people without regard to race, color, national origin, religion, sex, age, veteran status, or disability.

This document is author-produced (unedited).