Brown dust and algae visible in pool water

How to Get Rid of Brown Dust on the Bottom of a Pool?

Have you ever found that the water in your pool has turned brown? Worry not; here are the general procedures to get your pool’s water from brown to clear.

Brown pool bottoms are a common problem among pool owners. They are usually caused by external contamination, such as dirt and debris from neighbors’ gardens or storm waters. This leads to cloudy water, specifically during flooding periods. 

Brown pools can’t be ‘treated’ with other common pool water sanitation methods, such as algaecides or chlorine.


Understanding Brown Dust in Your Pool

Brown algae are one of the most common causes of brown dust on the bottom of your pool. They thrive in poor water conditions, particularly when chlorine levels are insufficient.

The brown color could indicate two main issues:

  1. Dead Algae: If you have trouble removing dead algae, it can appear brown in the water as it decomposes.
  2. Mustard Algae: If the brown dust reappears soon after removal, you might be dealing with mustard algae, also known as brown algae. This type of algae is highly resistant to chlorine treatments and can survive dehydration.

An in-ground pool with algae and brown dust on the bottom

The two most common causes of rapid algae growth in your pool are:

  • Warming water temperatures, typically in summer
  • Lack of chlorine

Additionally, if you’ve previously encountered algae, using the same vacuum hose, pole, or head can reintroduce brown algae into your pool.


How to Get Rid Of Brown Dust From Your Pool

Before you start, try to empty the skimmer baskets and remove as much debris as possible from the pool.

Step 1: Take Out And Rinse Your Pool Accessories.

Before cleaning the pool, remove all the items left on the pool’s edge, such as toys, floats, and other accessories. Mustard algae will cling to toys, equipment, and swimsuits, and these can regerminate the spores again in the water if they are not washed.

To eliminate algae, you can use chlorine-containing cleaners and/or algae-killers. Wash your swimsuits with color-safe laundry detergent and avoid using bleach.

Step 2: Brush Your Pool Surfaces

If you notice dirt at the bottom of your pool, then dirt is likely clinging to its invisible spots, including pool floors and walls. Shut down the pump and brush the entire pool. This is beneficial since brushing will help loosen the brown algae, making it easier for the shock to kill it and eventually vacuum.

It is recommended to use wire bristle brushes but regular nylon brushes for vinyl liners and fiberglass pools.

Step 3: Run the Pool Vacuum

Since you brushed down the pool, some of the dirt has either floated on the surface or sunk back to the bottom part. Brace yourself for some hard pushing ahead if you have a manual cleaner. If it is automatic, turn on the cleaner and leave it to do the work for you on its own. For example, Aiper vacuum cleaners channel as they circulate while scrubbing the pool’s bottom, sides, and ledges simultaneously.

Aiper robotic pool cleaner vacuuming the bottom of a pool

Step 4: Turn the Pump On/Filter System

Switch on your pump and make sure you let it run for some time longer than you usually do. You would like to remove that dirt before it finds its way to the pool floor, which is why you need to be using an automatic cleaner that sucks the debris at a given period rather than a manual cleaner that you have to control.

Step 5: Backwash the Filter

Brown algae can also exist in the filter, so it will need to be returned to its correct positioning by backwashing or cleaning it. Rinse the sand or media filter and clean the cartridge if it exists.

Step 6: Pool shocking or super chlorination

The next step is to add a shocking solution or chlorine into the pool as per the recommended dosage. With the help of superchlorination, chlorine can dissolve and eliminate resistant materials, chemicals, oils, and algae. Normally, these mustard algae could be controlled when the dose of superchlorination shock is 10 ppm. But shock, according to the water chemistry chart.

Step 7: Balance and Test Water Chemistry

It is also advisable that you balance your water’s chemicals with a water test while your pump is working. Dirt or any form of contaminant in your pool will disturb the balance of the chemicals in the water and may even promote bacterial growth.


Preventing Brown Dust from Returning

Keep your water balanced, and always treat your pool with a shock treatment, which will inhibit the growth of algae. Avoid the risk of reintroducing it by using a wheeled vacuum rather than brushes.

Other preventive measures include:

  • Cover the pool when not in use and clean up debris, fallen leaves, and other things that may fall on the pool instantly.
  • Clean the pool deck frequently by sweeping it or blowing it with a blower to sweep the fallen leaves that may have blown into the pool.
  • Check the pool equipment, as storms and power outages can malfunction.
  • To filter the brown pool, start the filtration system and leave it to work for several hours. Continue cleaning the filters until they are unclogged.
  • Maintain water levels
  • For existing algae, treat it with an algae-killer (over 60% in summers) according to the procedure recommended by the manufacturer. 
  • If “Flocking” the pool, add flocculent, circulate, and switch off the circulation system for 24–48 hours. Then, when dirt forms to bloom in the pool, it should be vacuumed to waste.



Yay or gross, you dismissed that dirt, sand, and mustard algae. If that contaminant was dirt, you’ve got a few easy prevention tools for keeping it out of your pool: Using a pool cover, ensuring that your filter is well backwashed or cleaned where necessary, and shocking the pool. A pool vacuum is handy for the dirt that would sink to the pool floor. If you have an automatic cleaner, you might not even need your hands to make it work.


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