Pentair MasterTemp 400 Common Problems [15 Easy Fixes]

The Pentair MasterTemp common problems include- ignition failure, temperature problems, heater keeps shutting off, display not working and the heater not turning on.

pentair mastertemp 400

Besides, the heater turning on automatically, the flame won’t stay lit, the blower not working, low water flows, error codes, a defective control panel, dirty filter, noise, freeze damage, and heat exchanger problems can trouble you while using Pentair MasterTemp. 

Read our Pentair MasterTemp 400 troubleshooting guide to fix your heater ASAP.

Table Of Contents

Pentair MasterTemp 400 Common Problems [15 Easy Fixes]

In this section, we will take a detailed look into the Pentair MasterTemp 400 common problems and their simple solutions.

1. Ignition Failure

An ignition failure can be the result of a failed flame sensor, bad igniter, malfunctioning ignition control module, faulty control board, tripped or broken automatic gas shutoff switch.

pentair mastertemp 400 bad igniter


You need to examine which part is malfunctioning. Then, replace the faulty heater part or parts. If the automatic gas shutoff switch has tripped, you need to reset it. 

2. Temperature Problems

There are some common temperature issues that users face.

temperature problems

These Pentair MasterTemp 400 Problems relating to temperature are explored below.

i) No Heat

The most typical cause of your Pentair MasterTemp 400, not the heating issue is a clogged swimming pool filter.  


Low water flow is the cause of up to 70% of all ‘My heater won’t heat’ service calls. Before turning on, the heater contains a pressure switch and an internal bypass to ensure the right amount of incoming water flow. 

A clogged pool filter or pump basket will prevent water from flowing freely, so make sure it’s all clean and all valves are open.

Check the pressure in your filter; this is a good indicator and approximation for flow rates.

ii) Displaying Wrong Temperature

Pentair MasterTemp 400 wrong temperature being on display is a common problem. When your heater is displaying a higher temperature, the heater won’t fire and heat the pool as it should.

Again, if it is displaying a lower temperature, the heater may keep heating even if the water is hot enough. This problem needs to be fixed ASAP.


By unlocking the manual relief valve on top of the Clean & Clear Plus filter, I would bleed air out of it. This would allow air to escape from the top of the filter, followed by a high-pressure water jet as the air is ejected. 

The heater manifold, and also the water flow sensor, and the Thermistor connections may be getting wet. Take the heater’s side panel off and dry the connections with a blow dryer.

Ensure that the control board is dry. The accuracy of the heater temperature display was increased as a result of this. 

iii) Overheating

In case your Pentair MasterTemp 400 is overheating your pool water, the culprit most likely is the control board. 


Look for a short between the Thermistor and the control board’s wiring. Contact customer service and tell them about the issue. They will help you out with replacing your control board.

3. Heater Keeps Shutting Off

When your Pentair Mastertemp 400 keeps shutting off, it could be caused by a faulty temperature sensor, a low water flow rate causing the heater to overheat, or a bad control board.

heater keeps shutting off


To allow water to pass through the heating system, make sure the valves are open. You can install a bypass valve to regulate the required flow rate.

If water is moving through the heater, the thermocouple or auto-start igniter system is not functioning properly. When the heater tries but fails to start, it recycles. 

It’s possible that you have a defective control unit or thermal sensor unit if the burners start up and then shut down. Replace the defective parts.

4. Display Not Working

Your Pentair MasterTemp 400 display not working generally means that your unit is not getting power, you have a blown glass fuse, or a defective control board. 

display not working


Ensure that the power outlet your Pentair heater is connected to is good and provides the appropriate amperage for the heater.

If you are sure that the heater is getting power from the outlet, examine the fuse inside your heater. Replace the fuse if blown.

Otherwise, your control board is most likely to be blamed. Test your control board with a multimeter. Replace in case necessary.

5. Heater Won’t Turn On

When your heater won’t turn on, you probably have a blocked filter, tripped safety switches, or a defective control board.

heater won’t turn on


A clogged filter or pump basket can build resistance to water flow to a degree that your heater can’t operate as usual.

Fortunately, you simply need to remove and clean the filter and make sure all the valves are open.

If the filter isn’t the issue, a faulty safety switch is next to check. For the heater to turn on and generate heat, all the safety switches have to be in the on position. In case the issue persists, replace the control board.

6. Heater Turns On Automatically

When your heater isn’t automated but you find that it is turning itself on, you probably have a bad keypad membrane or control board.

heater turns on automatically


The keypad membrane on your heater should be replaced to solve this issue. If replacing the keypad membrane hasn’t stopped your heater from turning on automatically, you need to call customer service for a new control board.

7. Flame Won’t Stay Lit

Your Pentair MasterTemp 400 won’t stay lit? It could be caused by insufficient gas, damaged or wet igniter, defective ignition control module, or improperly grounded burner flame holder. 

pentair mastertemp 400 won’t stay lit


Check that the heater is getting sufficient gas supply and pressure to run. Verify that the igniter is dry and not damaged physically. See if the igniter fires when you turn on the heater.

A sparking igniter is in good working condition. Otherwise, the igniter is bad and you need to replace it.

Ensure that the burner flame holder is grounded properly. Check your igniter module. You may need to replace it.

8. Malfunctioning Blower

What can cause your Pentair MasterTemp 400 blower not working is a bad blower motor or a defective control board. 

malfunctioning blower


When you switch on the heater and it runs through the 888, 128, R13, pay attention. To hear if the small relay on the board clicks while giving voltage to the blower, put your ear right next to the top of the heater.

Look at the blower if you hear a clicking sound. The blower needs to be repaired or replaced in this situation. The control board is the culprit when there is no click.

9. Low Water Flow

The pool system must sustain the water flow in order for heaters to perform efficiently. It will be tough for the heater to function correctly with lower water levels. This issue should be checked ASAP.


Ensure that the pool filter is clean and clog-free. Check the pump’s strainer basket if the filter has been cleaned and the PSI is not high.

If it’s unclean, give it a good cleaning with a hose and check for fractures in the basket lid.

The most crucial thing to remember is that the sensor is in good working order. Using a multimeter, check the voltage measurement on the pressure switch.

10. Defective Control Panel

Without a working control panel, your heater is no good. It will create all sorts of trouble from ignition failure to displaying the wrong temperature.

defective control panel

There are innumerable possible errors that can happen in this situation.


Test your control panel with a multimeter. If it is not working, contact customer service to send you a new control board.

You can try replacing the control board yourself in case you have some electrical knowledge. Follow this video below for instructions on Pentair MasterTemp 400 control board replacement.

11. Dirty Filters

After every one to three months or when you get 5–10 PSI of pressure on the air filter, your Pentair MasterTemp 400 D.E. filter should be backwashed. 

Also, at least once a year, you should disassemble and clean the D.E. filter. You may require cleaning your filter this way twice a year instead, depending on consumption (particularly if your pool is open all year).


You can clean your own pool filter easily. You need to take apart the filter cover and get the elements out. There are four of them. Wash them out very carefully with a hose. Once clean, put the filter back together.

Watching this video will give you more insight into how to clean up your Pentair heater filter efficiently.

12. Noise

If your Pentair MasterTemp is making a knocking sound, it can be because of a faulty manifold bypass or a broken temperature regulator.


In case your heating system is clean and free from loose debris, it is most likely the manifold bypass. Replace it.

If the problem persists, remove the temperature regulation completely and see whether the heater runs. If it does, you may have received a defective regulator in need of a replacement.

13. Freeze Damage

Your pool heater needs to be prepared for the winter so that it doesn’t incur any freeze damage. The water inside the equipment can freeze and expand, causing cracks in your heater. 


This kind of damage can be very costly. You will need to repair or replace damaged parts. So in this case, you need to prevent the damage.

To safeguard your heater from freezing temperatures, do two things. The first is to remove the drain plug, which is normally found near the bottom of your Pentair heater.  

Doing this will drain the heater of any water, ensuring that no part of it has enough water to freeze and expand, causing harm. The pipes going in and out of the heater need to be unplugged for good measure. 

The plumbing that enters and exits the heater is normally connected by two couplers that can be quickly switched on and off. Simply unplug these and turn them off for the winter.

14. Heat Exchanger Problems

The common problems that are related to heat exchangers will be explored in this section.

heat exchanger problems

i) Corrosion

Heat exchangers can corrode due to pinhole leaks on copper tubes, saltwater, lack of alkalinity, and low pH levels. 


Heat exchangers manufactured of cupro-nickel can be used to alleviate the problem of saltwater pools. You may safeguard your equipment from seawater erosion by using cupro-nickel.

Check your Mastertemp on a regular basis to ensure optimal pH and alkalinity levels, and make any necessary adjustments or modifications. 

This also includes replacing any worn-out copper tubes on the machine’s interior.

ii) Boiling

Boiling in the heat exchanger can occur for a number of reasons. The following are some of these issues and their solutions:

  • The water flow to the heater has slowed.
  • The exchanger is plugged in.
  • The bypass valve is still open.
  • The Thermal Governor has become jammed and is unable to open.


These are the possible solutions for this issue.

  • This problem can be resolved by servicing the pump or filter.
  • Change the water’s chemicals to achieve equilibrium. You might also bring the heat exchanger in for maintenance.
  • Get the bypass serviced.
  • Remove the old thermal governor and replace it with a new one.

iii) Leaking

A leaking heat exchanger is a serious situation. It can even be dangerous. 


Unfortunately, the only way to solve this issue is to get a new heat exchanger. But heat exchangers are expensive. They can cost you up to 50% of a new heater. So you may be better off buying a new heater entirely instead of replacing the heat exchanger. 

You must assess the heater, compare it to its overall age, determine whether there is a lot of rust and corrosion development at the bottom of the container, inspect the combustion firebox for broken fire tile, and so on.

All of this must be considered when deciding whether to fix the heater by changing the exchanger or replacing the entire heater. 

15. Pentair MasterTemp 400 Error Codes

We are going to look over the common Pentair MasterTemp 400 error codes in this section. 

i) Error Code E01

Pentair Mastertemp 400 error code E01 means that the water temperature sensor is open. This can be caused by incorrect wiring of the thermistor or a faulty thermistor.


First, you need to check on the wiring connection of the thermistor. The wiring diagram is given below for your reference. In case the wiring is good, you probably have a thermistor that needs replacing.

ii) Error Code E05

This error code means that the stack flue sensor is open. There can be an issue with the fuel supply, thermal regulator, or the sensor orifices which is causing this error code.

error code E05


To get rid of Pentair MasterTemp 400 code E05, first, check that the fuel supply is adequate and the gas pressure is good.

The thermal regulator should be in fine working condition. If not, replace it. Clean up all the flue sensor orifices to ensure there is no grime on them.

iii) Error Code E06

Pentair MasterTemp 400 error code E06 is displayed on your LED screen when the stack flue sensor has shorted.

When this happens, the front panel buttons will stop working. You will need to reset your heater to get it out of the lockout. 


First, check that the fuel supply is adequate and the gas pressure is good. The thermal regulator should be in fine working condition. If not, replace it. Clean up all the flue sensor orifices to ensure there is no grime on them.

iv) Error Code IGN

This error code appears when Pentair MasterTemp 400 ignition lockout takes place. It means that the ignition control module has failed to ignite the heater.


This problem has a very basic and straightforward fix. All you have to do now is double-check the burner. Here’s how to do it:

  • Press and hold the OFF button.
  • To get to the burner inside the heater, open it up.
  • Check to see if anything is stuck on the stove.
  • Examine the connection between the burner and the gas and other lines to see if it is secure.
  • In case the burner is broken, remove it and replace it with a new one.
  • Put everything back in its place.
  • This error code should not be shown on your Pentair heater at this point.

v) Error Code AFS

 The Pentair MasterTemp 400 error AFS appears on the display when the airflow switch is open.

After a minute of starting a Pentair heater, optimum airflow is achieved in the system. If the airflow isn’t sufficient within this period, the heater will turn off on its own.


To resolve this error number, ensure the fan is not obstructing airflow. To accomplish this, you must:

  • Turn the heater off.
  • Remove the cover from the blower fan.
  • Examine the area for any clogs or impediments.
  • Make sure the fan is completely empty.
  • Ascertain that the blower is securely fastened in its location.
  • Replace everything in its proper location.

As you turn on the heater, the error code should no longer be on display. 


What causes a pool heater to backfire?

Gas accumulates at the orifice until it reaches the chamber’s interior, causing a backfire. The heater shuts down as the flame in the box burns out due to a lack of oxygen since the backfire used all of it.

Can a gas pool heater explode?

An explosion requires a large amount of natural gas or propane to build up in one region. Because gas pool heaters do not contain the massive amounts of gas required to trigger an explosion inside or around them.

How do you test a Pentair stack flue sensor?

Turn on the resistance testing mode on a multimeter. Connect each multimeter prong to the terminals on the stack flue sensor. If the resistance is zero, the stack flue sensor needs to be replaced. The sensor is operating if the resistance is 3.5 ohm or above.

Why does my pool heater go on and off?

Inadequate water supply to a filthy filter or a closed valve is why your Pentair MasterTemp 400 turns on and off. 

Why does my pool heater keep tripping?

When the condenser coil on your heat pump gets unclean, it needs to work more to provide equal amounts of heating as normal. The breaker is tripped as a result of this. Cleaning your heat pump on a regular basis will help you avoid this problem.


Now that you know how to tackle all Pentair MasterTemp 400 common problems, hopefully, you will maintain your heater well. Maintenance goes a long way when it comes to heater shelf life.

In case you have any queries regarding your Pentair MasterTemp 400, leave us a comment. We will do our best to help.

About David

David is a man who loves doing research and finding out the best solution to any type of heating appliance issues like heaters and fireplaces. Whenever he finds the perfect solutions to any issues of heating appliances after doing in-depth research, he loves to share them with his readers. In fact, his aim is to help his readers to fix the issues with their heating appliances easily.More about us .

8 thoughts on “Pentair MasterTemp 400 Common Problems [15 Easy Fixes]”

  1. I have a Master Temp 400 pool heater it does not turn on. A pool technician replaced 3 sensors however it still does not work. The pool heater is about 4.5 years old. When it used to work I would hear a big kaboom sound and now nothing. Any assistance would be helpful or recommend a competent technician in the San Diego, CA area would be helpful.

    • Hi Robert

      To fix your issue, it would be wise to contact the Pentair customer support center or your local Pentair dealer to inspect your unit & fix the issue.

      Best of luck!

  2. We have a new Pentair Mastertemp 400. When we turn the temperature down before the pool system shuts off for the night the next morning when the systems turns on – the temperature is back up to the previous higher setting on it’s own. Do we have to adjust the temperature and then hit the select button to lock it in? Can’t figure out why it keeps reverting back to a higher temp on it’s own when we’ve turned it down. Any suggestions?

    • Hi Todd

      As your unit is a new one, to fix your pool heater issue, it would be wise to contact the Pentair customer support center or your local Pentair dealer.

      Wish you all the best!

  3. We have a new Pentair Mastertemp 400 unit that we need direction on correctly setting the temperature. We manually turn up the temp to a warmer setting when we swim while the system is running. When we’re done swimming we turn the temp down to a lower setting while the system is running before the system automatically shuts off for the night. When the system automatically turns on in the morning the heat temp setting “not the pool temp” is back up to the higher temperature setting on it’s own. Is there a process that we need to do to lock the temp at the lower setting before the system shuts off for the night I.e., when we lower the temp do we need to touch the select button? In short – the system keeps automatically turning the temp up on it’s own. Any help would be greatly appreciated. Thank you!

  4. I have a Pentair 400 master temp. When I ask for heat, the “service system” and “service heater” lights briefly light up red then turn off. Then i see a R9 code. It cycles for a bit then I hear a click either it fires off or it doesn’t. If no ignition, I turn off, wait, then re ask for heater. If it fires off everything works fine a few minutes then shuts off.
    Filter is clean


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