How to Clean a Waterbath (When You Can’t Avoid it Any Longer)

There’s something disconcerting about going to incubate a sensitive and irreplaceable sample in a water bath, only to be confronted by the Creature from the Black Lagoon. Unfortunately, water baths are an inviting habitat for all kinds of life, are often shared by many users, and are a perennially unpopular item to clean.  To help you overcome your fears of the monsters lurking in the water bath, here’s a quick guide to their cleaning and maintenance:

1) Emptying the nasty contents

First, disconnect the water bath from the power source and make sure the water temperature is safe to handle. If you’ve fallen behind on the cleaning schedule, it may be necessary to suppress your gag reflexes at this point. Large water baths usually have a drain outlet somewhere, to allow you to empty out the water into a container or sink. If the placement of the outlet is awkward, just connect some rubber tubing to redirect the water flow. Small water baths don’t usually have an outlet and must be carefully inverted over a sink, making sure not to get any water in the electronic parts. If you’re very unlucky, you might have a large water bath that doesn’t have a drain, which will require you to pump or siphon the water out. If you have to siphon, don’t ever get the water column started by applying mouth suction, because that would be incredibly gross.

2) Cleaning for function, not beauty

Clean the empty bath with soapy water and a cloth. If you can find the user manual for the water bath, you should check to see if there are any special cleaning instructions. You should never use bleach in a misguided attempt to sterilize a water bath, because it will corrode the stainless steel interior. Scrubbing with abrasives is also not recommended, since you can remove the protective coating from some kinds of water baths, and steel wool leaves behind flakes of metal that will rust. Also, don’t forget that you’re not polishing the water bath to make it look pretty; you’re just getting rid of microbial contaminants.

3) Filling with just the right water

When you refill a water bath, you need water that is not too salty, not too pure, but just right. Tap water is usually too impure and will lead to the build up of scale, and in some cases, chlorine corrosion. At the other extreme, the ultra-pure, deionized water from laboratory purification units (e.g. MilliQ or Barnsted ultrapure water) can promote corrosion, even for stainless steel. Instead, you should use a purified water that falls somewhere in between, such as singly distilled water, reverse-osmosis purified water, or whichever kind of purified water is plumbed into your building.

4) Keeping it sparkly between cleans

The only sure-fire way to keep a water bath clean and free of slime is to clean it regularly. There are commercial biocides available for use in water baths which can extend the time between cleans, but check that the substance is not going to affect your samples and that it doesn’t require special disposal procedures. One old trick is to throw in a small piece of copper tubing or a copper-plated coin, since copper has antimicrobial properties. However, never risk damaging the moving parts of a shaking water bath with loose bits of metal. Also, I would suggest keeping the copper out of direct contact with the steel, since this might exacerbate corrosion on stainless steel that has been previously damaged.

Finally, another option is to replace the water altogether, by using the metal beads sold by Lab Armor. These completely bypass the possibility of liquid contamination and can be used in most stationary water baths. You can’t use them for shaking water baths though, unless you like the sound of metal-on-metal destruction.

Those are my water bath cleaning tricks…what are your suggestions for how to keep the Creature from the Black Lagoon at bay?


  1. Mei on April 25, 2013 at 7:44 pm

    There are many products that work. Quats are easy to work with and you can adjust the concentration as needed. Q-Tabs/SpanTabs contains a blue dye that indicates it still active. For use in incubators, it’s important to get the right concentration. Find out more info at

  2. Gina Riggio on April 27, 2012 at 3:00 am

    That’s about the same as boiling distilled vinegar in your tea/coffee pot to remove calcium buildup. Works like a charm!

  3. seenabt on April 23, 2012 at 7:27 am

    Hi Christy,
    Nice article. Just last month we were struggling to clean our water bath which had accumulated a lot of scales. A friend suggested pouring 100ml acetic acid into the water bath (which had water) and boiling it for 30 mins. We left it overnight and cleaned the water bath in the morning….It was as good as new!!

    • Cristy Gelling on April 30, 2012 at 12:07 am

      That is a great tip! I’ve never tried it, but it as Gina pointed out – it works great for the lab coffee pot.

  4. Kurt Lager on April 20, 2012 at 11:40 am

    A little bit of sodiumazide has often been used to stop growth in waterbaths. But since that can form explosive compounds with some metals, I guess that’s also out of date now a days!

    • Cristy Gelling on April 30, 2012 at 12:03 am

      Yeah, I would definitely not advise using sodium azide. It’s also toxic!

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