Place a half-pound of pH reducer powder in a white sock. Drop the sock on the affected area for 30 minutes. If you see a significant change in color, then the problem is manganese.
Raise the water level in your pool until it is above all the stains.
Add muriatic acid. Use the amount according to a chart based on pool size and desired pH level. Watch the pH level until it drops to 6.8. Without lowering the pH level, you cannot remove the stains.
Brush the stains away once a day for two consecutive days.
Clean the filter. This will remove the manganese debris and help prevent the stain from returning quickly.
Add two to three doses of mineral treatment after all the stains have disappeared. The high dosage will destroy any remaining manganese in the pool.
Add soda ash to restore the pH from 7.4 to 7.6. Use a chart based on pool size and desired pH level to determine the amount.