Water Kefir: Anaerobic Method

by lydia on September 26, 2012

I switched to fermenting my water kefir anaerobically several months ago. Since water kefir is an anaerobic IMG_1513 ferment, I wanted the best vessel to ensure I was getting optimal health results out of my brews. I am quite happy with the consistent results I’ve achieved and am here to share how I do it.

There are many places online that will tell you to ferment water kefir by just using a cloth to cover it during the initial brew, much like kombucha. Since kombucha is an ‘aerobic’ ferment this is an okay approach, however not so for water kefir. I like how Lisa Herndon states it in her book; ‘Lisa’s Counter Culture: Pickles & Other Well Bred Foods‘, she says:


Most of the literature and certainly many food scientists and biochemists agree that lactofermentation is an anaerobic process. Anaerobic means fermenting food in an environment without oxygen. Many books with fermentation recipes have you doing this in less than ideal circumstances. Many recommend using a mason jar that is tightly sealed. Hmm…close but not really….the grooves along the top of a mason jar lid
allow for Grand Canyons of air compared to the size of the lactic acid bacteria trying
to dominate the container of vegetables or whatever we are attempting to ferment. If oxygen can enter, then this also means that mold and undesirable yeast can enter, too. This is not good. The point of fermenting is to create healthy LAB bacteria to repopulate our gut flora and improve our overall health.

Controlled ferments are made in anaerobic containers where airborne bacteria and yeasts cannot enter during the fermentation process.

I personally use 3 liter anaerobic vessel, like The Probiotic Jar ( a Fido base with a specially crafted lid) to brew my water kefir.

In the summer I tend to brew a bit more water kefir, but now that the weather has shifted we are drinking a little bit less. In the warmer months I brew about 9 liters per week of water kefir. My kids really go through it! It’s great too, because it is more probiotic rich and diverse than kombucha.

Water Kefir: Anaerobic Method
Recipe type: Beverage
  • Filtered water
  • Water kefir grains
  • Organic dark brown sugars (sucanat, rapadura or even brown sugar)
  • Organic Blackstrap Molasses
  1. To make 1.5 liters use this ratio:
  2. /2 cup water kefir grains
  3. /3 cup sugar
  4. -2 teaspoons molasses (optional)
  5. In a small glass jar dissolve sugar with small amount of hot water.
  6. Add the dissolved sugar water to the Pickl-It, fill halfway with filtered water then add the molasses if using. Stir well.
  7. Fill to shoulder with more water.
  8. Add grains, stir gently.
  9. Clamp down the lid.
  10. Add the airlock.
  11. Fill the airlock with 1½ tablespoons water.
  12. Place in a dark cupboard for 1-2 days.
  13. When ready, drain off the water kefir and reserve grains to make another batch.
  14. Now you are ready for your second ferment (see recipe in the post below).

IMG_0887 I store my grains in a 1.5 liter Fido jar in my fridge. Once a month, minimally,  I change the sugar water solution. Though every 2 weeks may be better – you can test to see how much of the sugar is still available before switching out the solution. So long as there is still sugar in the solution your grains will be getting fed. I add 1 cup of  organic sugar and 2 tablespoons molasses. It is possible to store your grains in a cupboard, but better to store your extra grains in the refrigerator if you aren’t able to monitor them frequently enough. Fidos can and will explode.

If you need to purchase fresh live water kefir grains, I recommend ordering them through Kombucha Kamp. I do not think it’s a good value to order dried grains -they take much more effort to get going and often are not succesful, your best bet is to start with live fresh grains.

After the initial brew of your water kefir is through, you can go ahead and bottle it up and drink it right away, or you can flavor it and do a second ferment. I always do a second ferment, I find it provides more flavor and effervescence. See my favorite way to second ferment our water kefir in the following recipe.

Vanilla Water Kefir


  • Finished water kefir from 1.5 or 3 liter Pickl-It strained
  • Vanilla extract (homemade is best, always choose gluten free)
  • Organic raisins (optional)
  • Wire stopper bottles (like a Grolsch bottle)
  • Funnel


  1. Line up your bottles on the counter.
  2. Place funnel in first bottle and add a dozen raisins.
  3. Then add 1/2 teaspoon of vanilla extract.
  4. Repeat with remaining bottles. (be sure to figure out how many bottles you will need based on your batch size and bottle size. They need to be at least 3/4 full each. I can get 6 Grolsch bottles full from a 3 liter batch).
  5. Once all the bottles are filled with the flavoring, slowly pour in the water kefir until full enough. Always save a little headspace.
  6. Clamp down the lids and place in a dark cupboard for 8 hours to 1 day.
  7. If your temperatures are much cooler it can go longer, just be careful and make sure you are paying attention to your bottles and checking to see when they are done. They can explode.
  8. Tastes like a vanilla soda to me! Yum!

If you have switched to fermenting anaerobically, as opposed to in random jars like mason jars, I can’t recommend my friend Lisa’s book enough. ‘Lisa’s Counter Culture: Pickles and Other Well-Bred Foods. There is no other cookbook out there that is full of recipes for using a Pickl-It or Boss Pickler. This book is so helpful, loaded with tips, conversions, and troubleshooting – I love it! It’s been a great resource for me as I continue to revamp all my old recipes as well as try new ones!
Click here to visit LisasCounterCulture and purchase a copy of her amazing ebook!

New to anaerobic fermentation? Here are the jars I recommend – The Probiotic Jar.


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Denise April 16, 2013 at 11:23 pm

Thanks for this! Could I just go ahead and do the second ferment in the pickl-it jar after I strain out the grains?

lydia April 17, 2013 at 6:42 am

You could – but remove the airlock at that point and use the plug-r.

Denise April 28, 2013 at 12:09 pm

Awesome, thanks! Is the sugar or raisins for increasing necessary for the second ferment or is it just for flavor?

lydia April 28, 2013 at 12:12 pm

If you add raisins or fruit to the second ferment, it’s for flavor.

karuna November 13, 2016 at 12:53 am

No, actually the minerals in the raisins can ferment in second ferment and create more carbon dioxide which means more carbonation.

Mindy W. August 5, 2013 at 3:21 pm

Thanks for the instructions! I have a question- Why do you brew your water kefir in an airtight container? Other instructions I’ve found recommend covering the jar with a coffee filter so that it’s specifically not airtight… I’m a little confused and my water kefir may be suffering! Thank you!

lydia November 25, 2013 at 9:14 am


I brew water kefir in an anaerobic environment for several reasons. For one, I want a controlled environment and want to avoid potential issues with mold – mold is controlled by lack of oxygen in anaerobic conditions. I’ve had mold in my kefir before without it being visible -it can grow in the presence of oxygen. I have 2 people in my family that are allergic to several molds -we would not be able to drink our water kefir if we did not do it anaerobically. I also brew kombucha in the same room,which can cross ‘contaminate’ and a scoby can grow if you are doing an ‘aerobic’ water kefir ferment. Also, I’m looking to get more lactic acid bacteria -which only happens in an anaerobic environment, and avoid some of the types of bacteria that come as a result of an aerobic environment which are undesirable.

I’ve also had far greater success with my water kefir since switching to an anaerobic environment, my grains thrive as well.

Janet September 10, 2013 at 9:45 pm

Lydia, since I’m on candida elimination diet I would skip adding the raisins in the second part, right?

lydia September 11, 2013 at 6:48 am

Yeah, just skip the raisins. It will still be tasty!

Amber Torres November 24, 2013 at 11:12 pm

I would like to brew my water kefir in my 3 liter Picklit because that is what I have. Would you please give me the sugar/water/kefir ratio for that container?

lydia November 25, 2013 at 6:07 am

1 cup grains, 2/3 cup sugar, 1-2 tsp. molasses (optional), fill the jar to shoulder with water.

Rhonda November 30, 2013 at 11:27 pm

Dear Lydia,

Thank you so much for sharing the info about water kefir. This coming Monday I will go to GoodEarth store to pick up a jar of water kefir grains. This will be my first time. I have no idea how much water kefir grains will be in the jar when I come this Monday. I have been searching on how to do it via internet. All of them mentioned to use coffee filter. I am interested to learn more about your method rather than coffee filter. I do not know where to get special type of glass jar that you have. I saw just airlock at Wine fermenting store but no glass jar that has clamp down lid. Where do I find that specific jar with airlock? Did you have to drill the center of the lid to put the airlock there? Sorry for the questions if the information was already provided. If so, please help me pinpoint the information or site so I can get one like yours. :-) I am *soooo* nervous and at the same time excited to start making water kefir because I am afraid of making mistakes. LOL. and I am excited because I want to break the habit of drinking coke and sprite. I hope I will love water kefir over coke/sprite. Do you have recipe similar to coke and or sprite? Thank you and hope to hear back soon.

Rhonda December 3, 2013 at 5:38 pm

I left my comment the other day but dont know what happened to my comment. I was saying that this will be my first try. Also I was asking if you have recipe like coke and or sprite. Anyway, change subject, I have some jars but I am not sure about the seal. I noticed your seal is white. Mine is red/brown seal. Do I need to get new ones? Since I dont know if the seal needs to be “BPA” free before I begin the project. Hope to hear back soon. Thank you.

lydia December 4, 2013 at 4:50 pm


Sorry your comment didn’t get posted as quickly as usual due to me playing catch up from the holiday! Anyway, this is NOTHING like coke or sprite -a far cry from it! However, I do think there are some cola flavored types of liquid stevia you could use to flavor it with.

If you are referring to wire stopper bottles with the red seal that is fine. I don’t think in this case the BPA is an issue, since the liquid won’t be touching the seal. Contact the bottle company if you want to know for sure though.

Marta February 28, 2014 at 11:10 pm

Where can you purchase these jars? I’ve been brewing a water kefit in mason jars, now I’m worried that I’m doing more harm than good? How to tell if there are “nasties” in there?

lydia March 1, 2014 at 9:15 am

Marta, There is a banner and a link in the post of the jars I recommend!

Berit March 20, 2014 at 3:25 pm

Hi Lydia

I just started getting into making water kefir. I’ve also read about the benefits of doing it in an anaerobic environment. What I don’t understand yet is this: Kefir is said to contain a lot of beneficial yeasts. Aren’t those getting starved together with the bad guys?

Ada March 31, 2014 at 10:54 pm

Hello, thank you for such an informative post. I do drink the kefir water, my family’s favorite is the ginger ale pop. Now I’m trying to learn how to use my extra grains as a face cleanser, I can’t find the recipe for it, I also have heard that it can be used for plants but I can’t find the formula for that either. Please let me know.
Inquisitive consumer, Ada

Ary March 9, 2015 at 9:53 pm

I just got a 1.5L Boss Pickler, but I only have 2 Tablespoons of water kefir grains. How should I adjust the recipe? Thank you.

lydia March 18, 2015 at 4:08 pm

You need more grains to really get started – you can try doing a 2/3rd batch to get the grains growing/going but your resulting brew may not be worth drinking.

Anonymous March 20, 2015 at 1:13 am

Thank you! One last question, I’m going on vacation for a week, what do I do with my grains then?

lydia March 20, 2015 at 8:04 am

I would put them in a sugar solution in a Fido jar in the fridge.

DeAnna April 21, 2015 at 2:39 pm

I have read that alcohol content of the finished drink would be higher brewing anaerobically vs aerobically. I am curious because I have been brewing with an airlock since I started –

mayah May 9, 2015 at 4:00 pm

Hi Lydia,

I do not have the fermenting jars yet that you suggested for the water kefir. But I do have a 64 oz jar that has the clamp down lid, where all the air is completely locked out. Will this be okay to use until i get the other jars?
I have been afraid to close them airtight as I was thinking it might pop the bottle.

Trish June 7, 2015 at 7:17 pm

do you know if there is a testing kit that I could buy that could test if the fermented veggies and kombucha I have made has the good bacteria in it?

lydia June 8, 2015 at 7:05 pm

Sorry Trish – no I do not.

frances September 6, 2015 at 8:01 am

Maybe not today and only next time but I look forward to reading anything about Kefir Milk as I make it and put a cheese cloth over the mouth of a jug with an elastic band. Is this wrong? I also make Kefir Cream Cheese with my Kefir Milk and loving it.
Frances from Sunny South Africa

lydia September 8, 2015 at 8:08 am

Hi Frances,

I used to do it that way myself but found it was best to do it in an anaerobic vessel. One of the biggest reasons I switched to this method is to avoid things like mold getting into my healthy kefir. True ferments need an anaerobic environment. Here is how I make milk kefir: http://divinehealthfromtheinsideout.com/2012/08/milk-kefir-anaerobic-fermentation/

Marcelo October 30, 2015 at 7:40 am

I did this change of envinronment intuitively. And I also put my drained kefir water in wire sealed bottles and store them in the fridge (I add more kefir every now and them just to keep it fermenting [It always has a bit of sugar left]). After some days fermenting, it tastes like alcoholic beverage, like beer or champagne.
My questions are:
Does it really get alcoholic?
Althought alcoholic, does it stilintuitivelyl has its probiotic properties?
Sorry if my post is not very clear, english isnt my first language…
Cheers from Brasil

Liz March 23, 2016 at 10:08 am

Hope you’re still answering on this post….
A few questions:
-when flavouring with fruit etc, do you put it in cheesecloth or anything to remove it from the grolsch bottler after the second ferment?
-optimal ratio for fridge storage for grains not in use? I think I over crowded my grains and they aren’t happy.
-how long can you store the bottled kefir for in the fridge?
-do you ever switch to a refined white sugar for a while? I think overcrowding and overmineralizing my grains might be my problem.

Andrea Avery December 12, 2016 at 1:40 am

Hi, I’m just getting started with water kefir. I’m using freeze dried grains from cultures for health. I have fermented these grains about 3-4 times now, but so far all I’m getting is sugar water. I’m using a probiotic jar, so I have the Fido jar and airlock. However, my end product does not taste sour at all. It just tastes like sugar water; very sweet. I’ve even tried fermenting for longer and at a higher temp. I read one site that said that since kefir has yeast and bacteria that it needs oxygen. Is this possibly why my grains are not making kefir?
Thanks so much!

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