Pool Troubleshooting /
How to Get Rid of Mustard Algae in a Pool
Mustard algae is stubborn, so get rid of it by brushing, vacuuming, cleaning the filter, and following label directions. Good circulation and routine care help prevent it from returning.
Archive date: this article was written for PoolSkimmer on Oct 23, 2026 and given the earlier archive date of Sep 11, 2026 so the blog reads as an organized archive. It was not published on that date.
The surest way to put an end to mustard algae is to do away with what is in plain sight and then put in the work on your filtration, circulation and general upkeep so it has no chance of a return.
How to eliminate mustard algae from a pool
A good place to start is a thorough physical cleanup. You will want to inspect the walls, ladders, the floor and any shaded corners where this type of algae has a habit of holding on. Brush those spots slowly and with care to dislodge it before it can re-enter the water.
There is a logical order to follow:
1. Skim off any leaves or floating matter to keep them from sinking. 2. Before you open the skimmer basket, make sure the pump is off. 3. Give the walls, fixtures and hidden edges a good brushing. 4. Put the vacuum to work on the debris you have loosened; be sure to consult your equipment manual for proper procedure. 5. The filter should be backwashed or cleaned in accordance with the manufacturer’s instructions. 6. Once you have the circulation running again, make daily checks until the water is clear.
When using a manual vacuum, take your time with overlapping passes as set out in the manual. Under no circumstances should one put a hand into operating suction equipment.
What makes it so difficult to remove?
It is a stubborn organism that clings on tight and will make itself at home in areas with weak flow. A dirty filter or poor skimming gives the algae plenty of room to settle. You are likely to find it in trouble spots such as:
- around ladders, slides and handrails
- in the shallow end or on the pool floor
- in the skimmer baskets and filter system
- in any corner or wall that is in the shade
If the water is looking cloudy, the filter or circulation is probably in need of some attention. Hayward’s own maintenance advice is that a clean filter and regular brushing are what allow the pool to run efficiently.
Is algaecide or shock the answer?
Chemicals have their part to play but they should not be a substitute for cleaning. Hayward points out that a routine shock will help rid the water of organic matter and algae, provided you test the water often and add chemicals only as called for.
Exercise caution in how you handle them:
- Adhere to the product label without deviation.
- Never mix unless the label says you can.
- There is no guessing at dosages or making up your own recipe.
- Put on the appropriate PPE.
Should you be in any doubt over which chemical is right for the job, a pool professional can safely walk you through the label and the test results.
Preventing a recurrence
Once the visible problem is gone, it comes down to routine. Make sure the water is moving and the filter is in good order.
Some useful practices are to skim often, brush the walls once a week, and let the pump run long enough for proper circulation. Adjust the chemistry according to the label after testing. Keep an eye on any leaf litter or shaded spots that could become a haven for the algae again. Fewer hiding places means less of a problem.
Time to call in a pro?
If the algae is persistent or the water will not clear, or if you are not comfortable with what the manual is telling you, get a qualified professional to look at it. Do the same if there is any sign of electrical trouble, damaged equipment or an unsafe suction condition. Leave electrical repairs to someone else and never go near a suction outlet. And always shut the pump off before you reach for the skimmer.
Sources and further reading
- [Hayward: Weekly pool maintenance](https://www.hayward.com/maintenance/weekly-pool-maintenance)