Why is my pool water yellow or brown? Iron, manganese, and tannin stains

Step 1: clear or cloudy?

Run the cloudy check first. If the water is yellow-brown AND clear (you can see the bottom of the deep end clearly), the issue is dissolved metals. If it is yellow-brown AND cloudy, the issue is mustard algae or organic tannins.

Metals make the water look like weak tea: tinted but transparent. Algae and tannins make it look like coffee with cream: tinted and opaque.

Metals: the most common cause

Three metals cause pool water discoloration. Iron stains yellow-brown to orange. Manganese stains purple-brown. Copper stains blue-green (and is rare unless the customer has been using copper-based algaecide).

Sources: well water used to fill the pool, corroded copper plumbing, copper algaecide overdose, deteriorating heater elements. In Arizona and parts of Texas, the municipal water itself has enough trace iron that levels accumulate over a few years of evaporation and refill.

Test with a metal test strip kit. Iron above 0.3 ppm causes visible staining. Manganese above 0.2 ppm is even more aggressive.

“Never shock a pool with high iron until you have added a metal sequestrant. Chlorine oxidizes the iron into permanent stains.”

The fix for metals

Step 1: add a metal sequestrant (the standard product is a phosphonate-based chelator, sold as "Stain & Scale Preventer" by most chemical brands). Initial dose is typically 1 quart per 10,000 gallons. Run pump 24 hours.

Step 2: test again after 24 hours. If staining is gone and water is clearing, maintain by adding 8 oz per 10,000 gallons every 4 to 6 weeks.

Step 3: address the source. If the customer is filling from well water, suggest a sediment + iron pre-filter on the fill hose. If old galvanized plumbing is the source, that is a plumber problem.

Mustard algae: the yellow-green case

Mustard algae is the rarer cousin of green algae. It clings to walls and steps in patches, looks yellow-brown rather than bright green, and survives normal chlorine levels. The visual signature is patchy not uniform; the water is slightly cloudy and yellow-tinted.

Fix: SLAM at the CYA-appropriate target (per the chemistry essentials chart). Brush walls aggressively to break up the algae layer. Use a mustard algaecide product on top of chlorine for the first 24 hours (mustard algae is resistant to chlorine alone). Pass the SLAM completion test before declaring done.

Tannins: the tea-stained case

After heavy rain, fallen leaves, or runoff from mulch beds, tannins leach into the pool. The water turns tea-colored, often clear at first then cloudy as biofilm forms. Common in autumn or after spring storms.

Fix: remove all leaves and organic debris immediately. Shock at 2x normal dose with 12.5% liquid chlorine. Filter 24 hours. If clarity has not returned, add a pool clarifier to clump fine particles. Tannins also respond well to a small dose of pool enzyme product (1 to 2 oz per 10,000 gallons).

What NOT to do

• Add chlorine FIRST when you suspect metals. Chlorine + iron = permanent orange stains on plaster
• Ignore copper algaecide history. Customers who DIY with copper algaecide for 2 to 3 seasons end up with permanent blue-green stains on the surface
• Use Vitamin C (ascorbic acid) on stains without testing first. It works on iron but reduces chlorine to zero, requiring a full rebalance
• Skip the metal test and shock anyway "to see if it helps". You may turn a $40 sequestrant problem into a $4,000 replaster

Pricing the metals diagnosis

Standard residential service call: $75 to $150 diagnostic plus chemicals at cost plus 25% markup. Initial metal sequestrant treatment runs $40 to $80 in product. If acid wash or stain removal is needed (existing surface staining), that is a separate $400 to $900 plus optional Vitamin C stain treatment. Always send a written estimate before starting.