Brown pool water is usually the result of too much dissolved iron, according to the Michigan State University website. This can cause major pool problems in hard water areas. If allowed to go unchecked, a high concentration of dissolved iron in pool water will stain the walls of the pool and anything submerged in the water. When iron is present, you should treat water with a sequestering agent and a pool clarifier. Both liquid chemicals are commercially available.

...
Brown pool water isn't nearly as inviting as clear pool water.

Step 1

Shock the pool using chlorine or bromine. Follow the manufacturer's directions on the container to ensure the pool is properly shocked. Shocking a pool with chlorine requires you to wait eight hours before beginning any other type of treatment. Shocking a pool with bromine requires you to wait only 15 minutes. After shocking, the water may appear darker brown. This is normal.

Step 2

Turn off the pool filter. If the filter is left on, the sequestering agent will not work properly.

Step 3

Apply a liquid sequestering agent to your pool while the filter is turned off. You can buy sequestering agents, which bind to iron molecules in a pool, through home improvement warehouses or at pool supply stores. Most require approximately 24 hours to work properly and will not remove all the brown coloring in the water. Follow all the manufacturer's directions to ensure the best results. Turn the filter on after the manufacturer's prescribed amount of time.

Step 4

Add a liquid pool clarifier to the pool after you turn on the filter. Like sequestering agents, pool clarifiers are at most home improvement retailers and pool supply stores. Follow the dosage and circulation time instructions on the clarifier's label. The clarifier will remove any brown coloring left behind by the sequestering agent. Do not swim in the pool until the appropriate amount of time has passed.