How To Clean Agates: A Beginner’s Guide

Cleaning agates can be a fun, but perhaps challenging, step in the rock collecting journey.

By the end of this article, you should know at least three different approaches for how to clean agates.

How To Clean Agates (EXPLAINED)

When you search online, it seems that just about everyone has their own method, and it is hard to know what you should try.

The answer is this: there is more than one way to clean an agate.

But rather than just sticking to the way every time, I would recommend that you formulate a strategy for cleaning up your precious specimens.

Not all agates are alike in form or composition, and what you are “cleaning up” is going to vary from rock to rock.

When Cleaning an Unfamiliar Rock, Start Conservative: Identify First.

Some people bring their box of rocks home and dump them straight into the utility sink full of water and Dawn dishsoap to soak.

Having learned a bit about malachite and some other specimens that contain copper and arsenic (which really shouldn’t be handled with bare skin or placed in water), I think the first step is to sort the rocks you’ve collected to identify what you have.

People sadly destroy cool rocks like geodes with acid because they didn’t stop to figure out what was holding the inside crystals together.

That way you can do any research you need to as far as what you should or shouldn’t do with the stone.

For example, some stones are not “acid safe.”

Now let’s say you’ve sorted your rocks, and decided that you have a nice pile of innocuous agates.

Your specimens might be coated with dark rust colored stains, or show white crustiness.

At this point, I would then place the rocks in a flat bottomed container and cover them with water.

Allow them to sit, and then spend some time scrubbing at them with a toothbrush or some other brush that isn’t too abrasive (won’t leave deep scratches).

If you like tumbled rocks, you could also put the agates in the tumbler to see if some of the stains (or all) would come off without having to resort to cleaning agents or acids.

However, not everyone likes the look of a tumbled agate, preferring instead the more rough and wild look of jagged pieces of agate.

After you have soaked and scrubbed your agates, let them sit out to dry fully. Then get a look at them.

If they still look dirty, or have dark or white spots, scrub the rocks with Dawn dishsoap and a scrub brush.

Again, rinse the rocks and allow them to dry completely before moving on to the next step.

Still don’t look the way you want? Let’s explore the options.

Removing White Buildup of Calcium

Once you’ve cleaned the rocks thoroughly, and the white buildup has not come off, you can try soaking the stone in CLR, (Calcium, Lime, and Rust Remover), or in a product called The Works, which is a toilet bowl cleaner that is popular among rockhounds.

(The links to products in this post are Amazon affiliate links. As an Amazon affiliate, I may earn a commission from qualifying purchases at no additional cost to you).

Allow the rocks to site for 1-2 days, then remove, rinse, scrub again with Dawn dishsoap if necessary, then rinse and allow them to dry completely.

If you don’t see any improvement, try another soak of CLR. If still no improvement, consider trying Iron Out (as noted below).

Removing the Dark Rust Colored Stain (or Stubborn Calcium)

Does the light colored (white/yellow/quartz) portions of your agate seem to be covered in places by run off from red parts of your agate?

Does it look rusty?

Do the cracks look like red lines?

One of the ways to resolve this discoloration is actually to soak the agate in a mixture of water and Iron Out.

To use the Iron Out on your agates:

  • Place your completely clean and dry agates in the bottom of a flat bottomed vessel. Don’t try to pack too many rocks into the Iron Out bath; give them some space in the container.
  • Add enough water to completely cover the rocks.
  • Add a few (2-3) tablespoons of Iron Out.
  • Wait, and observe. The process could take anywhere from a day to two weeks. Just watch the rocks as the Iron Out solution does its thing.
  • When they look ‘done’ pull the rocks from the solution, rinse with water, and discard the Iron Out. Some folks like to flush it down the toilet, to help the pipes perhaps?

One thing we don’t recommend you do is mix any of the various cleaning agents, either purposefully or inadvertently, unless you know what you are doing and trying to create.

One way you could inadvertently cause a dangerous chemical reaction is by putting a stone in one solution, and then moving it to another solution without completely cleaning it off.

Can You Use Vinegar To Clean Agates?


If you don’t like the idea of trying CLR, The Works, or Iron Out because they are very “chemical-ey,” another tried and true method people utilize to try and clean up their agates is a soak in a mixture of distilled water and white vinegar.

This feels like harsh on the environment.

Once you have soaked the rocks and are ready to remove them, you’ll want to neutralize the acid on the rocks with some kind of base.

A solution of water and baking soda would do the drink, while others might recommend milk (we never tried milk).

Other Methods To Clean Agates

There seems to be no end of ways to clean agates, such as:

  • Boiling the agates before scrubbing
  • Soaking the agates in bleach or a bleach solution
  • Soaking the agates in a citric acid solution
  • Soaking the agates in oaxalic acid
  • Soaking the agates in muriatic acid

Again, we aren’t being critical of any of the methods others are utilizing today.

That being said, as noted above, we do tend to start with the most conversation approach and work down towards the most aggressive (the harshest acids).

It is easier on the environment, and we are less likely to permanently damage ourselves or our homes.

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how to clean agates