Shocking your well to remove bacteria and contamination is an important job. I know the uneasy feeling you can get after finishing the process just to find brown water after shocking well water. However, you are not alone, and this is actually a quite common phenomenon that can be fixed by following the right steps.
Here I’ll take a look at some of the possible causes of brown water and sediment after shocking a well and how you can solve it quickly. Let’s get started so you can have crystal-clear water in no time!
Why You Have Brown Water After Shocking Your Well
Having brown water after shocking your well is not an unusual phenomenon. The chlorine solution used to shock the well reacts with reducing bacteria, iron, manganese, and sediment in the well which is then mixed into the water supply. That is the reason for the brown water color you see.
This is especially true if you have not disinfected your well for many years. Over time, wells can collect meaningful sediment and scale build-up. A strong shock treatment may dislodge this material and plug your well pump or cause damage in other areas of the plumbing system. That is why you may want to consider starting with a weaker chlorine solution if this is your situation. However, if done correctly, this is a great way to rehabilitate your well and increase the well yield.
Flushing the well water supply by running an outdoor spigot will typically resolve the discoloration. If the water runs brown or red, continue to pump it out while making sure it doesn’t recirculate back into the well. Sometimes you may need to flush the system for several hours, or over the course of a few days for it to completely go away.
Note: If you use a chlorine solution that is too strong, it makes the water highly alkaline which can not only lead to brown discoloration and sediment, but also reduce the overall effectiveness of the shock disinfection treatment.
Other Primary Causes of Brown or Rust-Colored Well Water:
There are a number of issues that can cause brown water. Here is a list of other primary causes your well water is turning brown after shocking it:
- Iron Bacteria: If well water contains high iron levels, it encourages the growth of iron-oxidizing bacteria, which get their energy by oxidizing the dissolved iron in the water. Large amounts of iron bacteria lead to an orange, red, or brown slimy film that can wreak havoc on plumbing systems. The bacteria growth can also lead to unpleasant odors.
- High Levels Of Iron: Water that’s brown or rust-colored is likely to contain ferrous iron. This dissolved type of iron changes forms when it is exposed to air and is oxidized. Even iron concentrations as low as 0.3 PPM can lead to brown water staining. If your water still appears brown after shock chlorination, it has high levels of iron, which you can remove in other ways. Although iron in your water is not dangerous, it can harbor harmful bacteria growth.
- High Levels Of Manganese: If your water supply has a deep brown or blackish color after shocking it, chances are there is Manganese present. This can come from the water supply or corroded pipes. Similar to iron, manganese does not have a regulated safety level, but the EPA set a secondary contaminant level of 0.05 PPM to protect against black and brown staining.
- Deterioration Of The Metals In The Well Structure: Aging wells will deteriorate over time. The metal components used can rust and break away into the well water supply. In severe cases, the well may begin to collapse. Regular testing and maintenance is the best method to extend the useful life of your well.
- Contamination From an Outside Source: If your well is contaminated from an outside source, the water will continue to be discolored. If you have flushed your system over the course of several days and still experiencing brown water, you need to inspect your well. Closely examine the well head, seals, and any exposed infrastructure that may have cracks or leaks.
- Earthquakes Or Flooding: Natural disasters can cause massive changes in your groundwater supply. After earthquakes or flooding, it is not uncommon to see changes in your water quality. It is suggested to monitor and test your well water to ensure it reverts to in original condition.
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What About Sediment in Water After Shocking a Well?
You may find sediment in your water after performing shock chlorination. When you perform shock chlorination, you run chlorinated water throughout your entire water system which can dislodge rust or scale from the pipes. If this happens, the rust and scale can circulate in your water.
Adding chlorine will oxidize the sediment and cause the water to turn brown or rust-colored. If you have a sediment filter, you should examine it after the shock chlorination treatment to ensure it is not clogged.
Additionally, the chlorine agent will treat organic substances, but it will not remove sediment or debris. This is why it is critical to thoroughly pump the well after chlorination to keep the sludge and sediment out of the plumbing lines.
More often than not, between flushing your system and giving time for the sediment to settle, your water supply will become clear within a few hours.
Proper Chlorine Disinfection Protocol
As discussed earlier, it is very important to carefully follow the disinfection protocol during shock chlorination. Not doing so could cause your water to fail to be disinfected. Or, it could become reinfected due to failure to thoroughly flush the water system. If the water is not sufficiently circulated throughout the system, it could also cause your water to appear brown.

How To Fix Brown Well Water After Shocking
If you have chlorinated your well and you find your water is brown, here is how to fix it.
- Make sure you have the correct bleach. The bleach should have a chlorine concentration of 5% to 5.25%. This is necessary to kill any bacteria or algae in your water. Additionally, be sure you use new bleach since bleach will become less effective over time. Also, don’t use scented bleach because it may have chemicals you would not want in your water system.
- Identify what is causing the contamination. If you believe an outside source is contaminating your water system, you’ll need to find the source and resolve the issue, or your water will become brown again. It could be as simple as a broken seal or lid.
- Use the correct amount of chlorination. It is important to avoid using too much bleach that you damage your pipes. Furthermore, if too much residual chlorine interacts with organic substances and iron in the well, the effectiveness of the disinfection will be diminished. On the flip side, make sure you use enough to kill the bacteria. If you didn’t use enough, you might need to repeat the shock chlorination. As a general rule for chlorine concentration, use 3 cups of bleach for every 100 feet of well depth.
- Let the chlorine solution work for a sufficient amount of time. It is best to give the chlorine solution at least eight hours to work, and leaving it overnight is even better.
- Replace your water filters. Your water could have high iron due to rusty pipes and plumbing, which can cause your water to look brown. If this is the case, your water will turn brown again after shock chlorination. But, with the right filters, you may be able to filter out this iron. Check your sediment filter to ensure it is not clogged.
- Check Water Softener Media: If you have a water softener, the broken resin beads may be the cause of persistent brown water. The broken resin beads make their way into your water supply. The best way to resolve this is to replace the water softener media.
- Remove faucet aerators while flushing your water system. Shocking can dislodge scale and rust that might have built up on the pipes. This could get caught in showerheads or faucets. If this happens, it could cause your water to continue to be brown, But if you remove the faucet aerator during the flushing process, it should let any chips of rust or scale that would have been stopped by the aerator flush through the system.
- Thoroughly circulate the water. Be sure to run water through all of the faucets in your water system. If you fail to do so and any faucet remains dirty, the water could turn brown again.