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Community and Q&A

Disinfecting a Smelly Whole House Water-Filtration

BenSki33 | Posted in General Questions on

We installed a whole house filtration system in November. We already had a water softener and kitchen RO. About 2 months later we started getting very smelly toilet tanks and now our hot water and water softener brine tank are smelling bad too. Does anyone know how to disinfect these items and who could help? Has anyone heard of this happening? We are on city water.

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  1. Jon_R | | #1

    Does your whole house filtration system remove chlorine? Chlorine serves an important purpose (eg, preventing downstream bacteria growth and the resulting smell).

    I tried cleaning and temporary chlorination - the smells just came back.

  2. BenSki33 | | #2

    Yes, it does.

  3. Expert Member
    BILL WICHERS | | #3

    You would need an activated carbon filter to remove chlorine. Particulate filters won't do it, and neither will a water softener. I'm pretty sure an RO system will remove cholorine, but I haven't checked to be certain. Chlorine WILL damage the resin in the water softener, and the RO membrane though, so there is a good reason to strip the chlorine before it runs through these devices.

    You should have a particular filter ahead of everything as your first filter. This will protect things like the water softener from clogging with any sediment in the line, and even city water does have some. I like the Pentek "Big Blue" filter housings and the 2501 filter cartridge for this purpose. If your city water is pretty clean, and it probably is, you can save a little money using the 1/2 size filters which are half the length of the Big Blue size (you need the smaller housing to use these). You can put in a second housing to hold an activated carbon filter to remove chlorine.

    Is the smell a rotten egg type of smell? If so, this is from sulphur, and is usually from a bacteria. It's not harmful, but it makes for a lot of stink. You'll need to sanitize your softener and the pipes, which can be done with bleach. It's not difficult to do. A pretty decent how-to for doing this is here:

    There are several types of anode rods for water heaters, magnesium, aluminum, and a zinc alloy. You don't want to REMOVE the anode rod, even though some places say that will help, because that anode rod is there to protect your water heater's tank from corrosion. What you want to do is try one of the other types of rods to see if it reduces your smelly water problem.

    To minimize the chances of this smelly water stuff happening in the future, you need some extra filtration steps. An activated carbon filter alone MIGHT be enough, but if you have a lot of sulphur in your water, you'll need a manganese greensand filter. I use one of Pentek's RFFE20-BB cartridges on my well, and although it says it's for iron, it will also remove other things it reacts with, including sulphides. It's not cheap, and you'll have to replace it periodically, but it does a very good job.

    If you have a lot of iron in your water, that can be an issue too. Iron will cause orange staining, and there is an iron fixing bacteria that can also contribute to smell and orange slimy coatings. It's not harmful, either, but it causes smelly water. The Pentek iron reduction cartridge will help with this too. If your softener has been stripping out the iron for you, your resin might be clogged up with iron, in which case you want to run some Rust Out through the water softener to clean it.

    If you have iron problems, it is important to do the Rust Out step on your softener BEFORE you santize it with bleach!

    Note that these kinds of water problems are all pretty common for people on wells, so there are plenty of products out there to deal with things -- you just need to know what you're starting with. You could have a water test done, but on a city water system you can just ask your water authority for a water quality report and that will tell you what's in your water. Once you know what you're dealing with, you can design a proper filter system.


  4. BenSki33 | | #4

    We have high bacterial counts in our water now, including showers, faucets, and softener. I did disinfect the softener and it got better, but still has some bacteria. Does anyone know what companies can help with residential chlorination? We are on city water and don't have a well but we did install a whole house filter which removed all the chlorine.

    1. Jon_R | | #5

      You could simply remove your whole house carbon filter cartridge, which will leave the needed chlorine in the water.

  5. BenSki33 | | #6

    Unfortunately we already bypassed it for 6 weeks and we still have high levels of bacteria in the water. The chlorine level is now testing at 0.26 inside and 0.5 at the outside from city

  6. Expert Member
    BILL WICHERS | | #7

    With the chlorine filter bypassed, flush your system -- continously run the water from ALL taps for at least a few hours, possible a day or more. Let the chlorine kill things, but the circulating water remove contaminants.

    Bacteria are sneaky and like to hide out in places that don't get flushed out. Make sure your water heater is hot enough (I'd drain it and refill with chlorinated water too, otherwise it will take a long time for chlorine levels to build up in the tank), and make sure you didn't miss any water taps when flushing the system (outdoor taps, humidifier, laundry, etc.). Any stub on the pipe that doesn't circulate water could be a resovoir of contaminants. You need to make sure you flush EVERYTHING.

    I would probably drop one of the clorox tabs in each toilet tank too. Sterilize the softener again too.

    The tricky part is if you don't do things in the right order, you keep reinfecting your system, basically. Once you have chlorinated water flowing again, you need to disinfect each downstream thing in turn, starting at whatever is closest to the water source and working your way "downstream". If you go backwards, you just reinfect things downstream.

    If none of that works, you can put some bleach in your first filter cartridge and use that to "shock" the system with a very high level of chlorine (look up "shock your well" for info on how to do this, the principle is the same for a well as it is for city water). What you basically do is use bleach (basic bleach, not anything fancy) in the well, or the first filter cartridge, then run the water out of each tap until you smell bleach, doing each tap one by one. After you have "bleachy water" everywhere, let the system sit for a few hours, then flush the ENTIRE system. That should kill any bacteria that are hiding out in the system.


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