Salt Chlorinator Trouble Shooting

Salt Chlorinators can be a tricky thing. With all those flashing lights it can be hard to understand what is going on. Here are a few tips on how to be sure that your salt chlorinator (Pentair Intellichlor) is working properly in your inground pool.

First and foremost ensure your chlorine output is set correctly (start around 50% and adjust as needed) by following this video if you have an Easytouch panel: Chlorine Output – YouTube or by pressing the less or more buttons on the cell itself if you do not have an EasyTouch panel.

If the chlorine levels seem low or like they are disappearing right away, you may have some of these issues:

  • High phosphates in the water: A chemical can be purchased at your local pool store or through us to remove higher than normal levels of phosphates.
  • The runtime on your chlorinator may be set too low: The newer chlorinators can run under 10% of the time. For percentages above 10% a solid light will indicate the current percentage. If one of the lights is flashing, it means the chlorinator is running at that percentage divided by 10, so a flashing 60% means 6% and so on. To make sure you are running at 60% and not 6%, press the more button until you have the solid green light.
  • An acid wash may be needed: This should be done at least once per season especially if you are on well water (we provide the service at openings and closings and sell the caps for you to do yourself.)
  • Make sure your salt level is around 3400ppm: 100-200 off may still work, the light under “Salt Level” that is next to the “Good” label should be solid green if your salt level is good.
  • Your salt cell is not functioning: If the cell is producing chlorine, even a small amount, then it is working. The best way to determine if your cell is functioning is to test the water with your test strips, then do a super chlorinate (100% output) for 12-24hrs, then test the water from one of the jets. If the test strip shows up any chlorine, even a minimal amount, then the salt cell is working.
  • Low temperature: If the water is too cold, below 70°-65° F (21°-18° C), your chlorinator will not be able to produce chlorine even if your salt level is perfect.

Salt Chlorinator Flashing High or Low Salt:

  • Make sure to test your salt levels and adjust it to around 3400ppm. if the salt level is off, the salt chlorinator will not work. High salt levels can also damage the cell and the rest of the pool equipment

No Flow Light Flashing:

  • If the flow light is red, then you need to pressure wash your cartridge filters. This is especially common during times of the year were there is high amounts of pollen. Even if the filters do not indicate a cleaning on the pressure gauge, they still need cleaning as pollen won’t show up as debris. An acid wash may also be needed to resolve this issue.

0ppm of salt showing on EasyTouch panel:

  • If this is the case and all the lights are green on the salt cell, do not add more salt to the pool. The cell is the true indicator of whether your salt level is correct. Get the water tested at a pool chemical supply store and if the levels are all correct, around 3600ppm, you can call us to book a service call. The cell will still work properly if all lights are green, but a part may need to be replaced by our technicians for it to communicate properly with the EasyTouch panel
  • If the water is below 70°-65° F (21°-18° C), your salt cell may not be able to send the salt ppm reading to the EasyTouch panel. Check your EasyTouch panel reading again once the water is over 70° F (21° C) to see if the temperature was the issue.

Check Cell Light Flashing:

  • This problem occurs typically in salt cells over 5 years old. Essentially, it means that the cell has reached its maximum amount of running hours and needs to be replaced. We stock the IC20 and IC40 Pentair Intellichlor salt cells here and can have one ready for you most days of the week even on short notice.


  • The filters may need to be replaced if you are having to clean them more then 2 or 3 times a season. They usually last about 3-5yr, possibly longer if there is not a lot of sunscreen and oils in the pool. If you soak the filter in filter that you can get from your local pool supply store it can extend the life of the filters.
  • The lights will flash upon start up of the pump until the cell registers the correct levels of salt and water pressure, this could last about 5-15mins

CAUTION: Whenever adding salt to the pool make sure your chlorinator sanitization output is turned down to zero for about 24hrs when only adding one bag of salt. On initial opening of the pool, it needs to be down to zero for about 36-48hrs since it will take more time to dilute in the water. This is done to avoid damaging the flow switch which also regulates the salt reading, the pool school videos explain more on how to increase and decrease the sanitization output or chlorine percentages.

No flow issues are 99% of the time fixed by pressure washing your filters even if the pressure gauge does not indicate this, as algae will not clog up the filter canister as dirt and debris would, but can still cause flow problems. You may also need to reprime your pump as it may have too much air in the lines or has lost suction. These videos can be very helpful to resolve your issue without needing a service call.

How To Fix Flow Issues – YouTube

How to Prime Your Pool Pump – YouTube

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