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How to Clean, Sanitize, and Store a Water Filter in the Off Season

It’s important to clean and sanitize your backcountry water filter or purifier before storing it away during the winter months. There’s a simple three-stage process for this that involves cleaning the filter to improve its flow rate, sanitizing the filter to kill any microorganisms inside it, and drying it before storing it until you’re ready to use it again.

Step 1: Backflush Your Water Filter or Purifier

Many backcountry water filters and purifiers can be backflushed, which means reversing the normal flow of water through the filter element. This serves to unclog any debris or contaminants that are stuck in the filter, flush them out, and improve the filter’s flow rate. Many filters and purifiers come with a hose or a syringe, like the Sawyer Squeeze that you can use to perform this backflushing operation. Still, others require that you “shake” the filter element, like the Platypus QuickDraw or the Katadyn BeFree when attached to a full bladder to clean it.

If you’ve used your water filter or purifier recently, you only need to perform the backflush/cleaning operation a few times to clean it out. If you haven’t used it recently and the filter element is “dry”, it’s best to run water through the filter in the normal direction to wet it out before commencing the backflushing operation.

Try not to exert any extra pressure when you backflush the filter element because it can rip or deform the internal filter element, which may just be paper, depending on the product you use. Sawyer claims their filters are pretty tough, but others are not, and I think it’s prudent to be firm but gentle during the backflushing process.

Step 2: Sanitize the Filter Element

In this next stage, you need to sanitize the filter/purification element and kill any microorganisms that may remain inside. You don’t want these to keep growing over the winter because they can permanently clog or damage the filter element. Different manufacturers suggest slightly different procedures for this process, so check their website recommendations.

But the two most common ways that people sanitize their water filter/purification element are to flush it with a diluted bleach solution made using one capful of fragrance-free bleach per Liter of water or to mix up a liter of water treated with chlorine dioxide made using Aquamira drops or Katadyn Micropur tablets. Filter these like you would raw water in the field and you’ll sanitize the filter element.

Step 3: Drying and Storage

Let your filter/purifier dry out slowly and naturally by placing it in a warm and well-ventilated location, out of direct sunlight. After a week, move it to a drawer or closet in the heated part of your home. Come spring, it will be ready to use.

Note: Some manufacturers suggest slightly different procedures for this process, so check their website recommendations. For instance, rather than letting your filter dry, some recommend storing it wet after it’s been sanitized, like the Platypus QuickDraw in the video above.

That’s all there is to it!

Updated September 2022.

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  1. Does the MSR Guardian need this treatment?

      From the manual:

      When to sterilize: Sterilize the Purifier before and/or after long-term storage to
      ensure long life and fresh-tasting water. Also sterilize it before any disassembly.
      1. Mix a solution of 2 mL (~1/2 tsp) of household bleach (free of dyes or perfumes)
      with 2 L of water, or dissolve 12 MSR Aquatabs® tablets in 2 L of water.
      2. Pump most of this solution through the purifier, stopping before air can
      enter the pump.
      3. Wait 30 minutes.
      4. Pump 1-2 liters of clean water to clear any remaining solution from pump.
      5. Pump the Handle to purge excess water from the Purifier.

  2. Just what I needed, an easy step by step way to do this. I’m wondering if there’s anything else I could use besides bleach? Our Sawyer filters were rank last year even though I backflushed and dried them, because I didn’t sterilize them. I’m just not a fan of bleach, but I could look at Aquamira drops. I wonder if I could try an essential oil that sanitizes?

  3. I just purchased a HydroBlu Versa Flow Water Filter. Over the phone one of their customer service representatives recommended that I santize this filter with a vinegar solution – 1 part distilled white vinegar to 3 parts water.
    Perhaps if you don’t want to use bleach to santize your filter, you could purchase a HydroBlu Versa Flow and santize with a vinegar solution.

  4. I’ve had a couple of stubborn Sawyer filters that after backflushing, drying and storing the next summer were difficult to use. I soaked them in diluted vinegar and then they worked great. Does anyone know if the vinegar compromises the filter in any way?

  5. Filters with a small pore size are susceptible to clogging due to hard water deposits. Most drinking water will have some divalent cations (Ca+2, Mg+2) that forms insoluble carbonate salts (from dissolved CO2) when it dries. The reason to rinse with vinegar is that the acid in vinegar (acetic acid) will dissolve the carbonates salts because carbonate is a base. It reacts with the acid to form soluble acetate salts and carbonic acid that decomposes to form CO2 again (mix baking soda and vinegar if you want to see the reaction). However the salts take some time to dissolve. So what I do is to run some vinegar through the filter, seal it, and let it set for a while (an hour or so), then flush that out and repeat until you get a good flow rate. Then run a large volume of tap water through it to get rid of all the vinegar. Then you can run a bleach solution if you want (I have never found this necessary if you have do a good job back flushing, vinegar washing, and rinsing). Finally you need to flush it well with DISTILLED water. Make sure it is distilled as this will be free of ions that will precipitate and re-clog the filter on drying. Reverse osmosis purified water might work, but I only trust distilled water. After the distilled water rinse, you can dry. I have used the same Hydorblu Versaflow filter for several years using this method. Still works like new. I prefer this over the Sawyer as it has threads on the clean side, making it easy to gravity filter into an empty bladder and back flush with no connectors, adapters, or syringes.

    • Odd man out: Thanks for the very logical and detailed procedure. I appreciate posts from someone with (apparently) a chemistry background!

  6. I was not sure what bleach to use so I emailed Clorox to find out which one of their products are fragrance-free and one that I can use in my water filter . A rep got back and said I can use Clorox performance bleach with cloromax or Clorox disinfecting bleach. hope this helps

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