content is free. We earn a commission at no extra cost when you purchase through referral links on our site.
Learn more

Brown Well Water After Heavy Rain – 5 Causes and Fixes

brown well water after heavy rain


Suppose the rain stops, and you make a cup of tea while adding tap water to it. In a first sip, you split it off due to its bad smell and unpleasant taste. You may think the rain is a wrongdoer for causing it. 

Yes, Heavy rains add sediments, tannins, minerals such as iron and manganese, fecal dirt, and corrosion into the well water, which lowers the water quality and taste. No matter whether it’s heavy rain, storm, or flooding if your well water has turned brown or leaving brown stains on your fixture, you need to take it seriously. 

In this article, we’ll let you know about the main causes of brown well water and the best solutions to fix them. Start with it!

Does Heavy Rain Affect Well Water 

Yes, heavy rain affects the water quality and safety of well water in various ways, such as lowering the water pH, making it more polluted and harmful to consume. When it rains, the signs and symptoms of affected well water include:

  • Stains on laundry, sink, toilet tank, and all fixtures
  • Yellow or brown water
  • Unpleasant taste
  • Metallic or foul smell
  • Colonies of slimy, dirty sludge material in wells, tanks, pumps, or toilet

Why is My Well Water Brown All of a Sudden? 

When it rains, the well water turns brown overnight due to high sediments, surface run-off including fecal dirt, mineral leaching, tannin formation, and corrosion of appliances. 

Detail of each cause is mentioned below:

1. Elevated Levels of Sediments

Heavy rains or floods contribute greatly to the addition of sand, silt, and dirt particles to the groundwater, which flows through the well. Especially when a new well is built, the well structure is damaged, the well is very old, your well is not properly protected, or the land around it is damaged.

Generally, the muddy water after rain doesn’t pose any health threat to humans and pets; however, it gives aesthetic issues such as musty, smelly, unpleasant taste and muddy water. Notice if you have encountered mud, settle down if you pour water into a container after heavy rain.

2. Surface Run-off From The Rain

The surface run-off from the rain is one of the frustrating inconveniences that most well-water users face. Along with the rainwater, contaminants such as soil, heavy metals such (as arsenic and lead), minerals (such as iron, magnesium, and calcium), microbes, fertilizers, pesticides, nitrates, and tannins seep through the well. As a result, the well water may take on a brown or turbid appearance.

When it rains, the water from the ground combines with the sewage leaking or fecal contamination, leading to brown well water. This fecal contamination can introduce various harmful bacteria such as E.coli or coliform bacteria, viruses, and other pathogens if the well casing is not properly sealed or if the well is located in an area prone to flooding.

According to a study, there are 265,000 STEC infections in the US each year. For more than 36% of these cases, E. coli O157:H7 is to blame.

You can’t see the contamination, but various serious health issues are hidden in well water. If you’ve noticed someone having diarrhea, nausea, vomiting, hepatitis, and typhoid after drinking water, the above contaminants can be causative agents. 

3. Mineral Leaching from Soil, Such as Iron and Manganese

Sudden brown well water can be a result form from mineral leaching, such as iron and manganese, from the soil. Heavy rain, flooding, or other environmental factors can exacerbate this issue. 

In areas where the soil contains significant concentrations of iron and manganese, rainwater can dissolve these minerals, allowing them to enter the groundwater and make their way into the wells. When these minerals are exposed to oxygen, they are oxidized and turn the well water yellow. Here is a complete guide on causes and solutions of yellow well water; read if you have this safety concern. 

These minerals are not harmful to consume but give an unbearable taste, unpleasant smell, and brown appearance to water. The presence of these minerals stains and clogs your laundry, plumbing fixtures, and even hair and skin. 

4. Development of Iron Bacteria

Think if you have examined the slimy orange sludge-type appearance or brown water in the toilet or any other area where water is allowed to stand for long after rain.

It happens when bacteria and fungi come into contact with the iron and start living with it, and they form clusters or colonies that you can see while floating on top of the water, such as a toilet tank. If yes, our guide for getting rid of iron bacteria from the toilet will assist you in this scenario. 

It is the most widespread cause due to increased water table and leaching of iron after rain. It can also be seen in wells, pipes, and plumbing systems, particularly in areas with iron-rich groundwater in the form of rust and biofilms. 

Over time, Iron bacteria’s metabolic activity can cause pipes and well parts to corrode, which could cause infrastructure damage and raise maintenance expenses.

5. Corrosion of Pipes and Pumps

Rainwater, and more specifically, the acidity of rain, can cause well components to corrode. It happens as a result of the presence of other pollutants and acidic compounds in the atmosphere. 

This acidic water interacts with the well casings, pipes, and other components. It can dissolve the protective layer present on the surface of well components and ultimately expose it to corrosion. Over time, corrosion can weaken well components, making them more susceptible to damage or break. 

How to Fix Brown Well Water? 

How to Fix Brown Well Water

You can treat the brown water by determining the main cause of contamination. Firstly, you can disinfect the well; secondly, choose the right type of treatment system, such as a sediment filter, iron filter, or a water softener. If you have multiple concerns, the reverse osmosis water filter system with pre and post-filters will be worth considering. 

Here is a simple guide on how to fix it:

1. Disinfecting and Flushing the Well

The first most cheapest method you can do is disinfection, which can be done by using regular home bleach or chlorine. It will help to kill all the microbes present inside and iron bacteria as well when water is allowed to stand with a high concentration of chlorine for 24 hours. 

It is important to note that it is not a permanent solution, but you can maintain the well by flushing it periodically. 

2. Sediment Filter – Best for Rust, Sand, Silt, and Mud 

After testing water quality at home or laboratory, if the presence convinces you of sand, gravel, rust, or any suspended practical, then considering a sediment filter for city or well water will be a perfect choice. It can filter out small to large particles depending upon their 1-200 micron rating.

If your water quality is affected by hardness, heavy metals, or elevated levels of iron, then the sediment filter alone will not be enough to fix the issue. For better results, we suggest you use a sediment filter as a pre-filter before reverse osmosis filter, ion exchange, or whole-house water filter at your point of entry. 

Check out our list of sediment filters that are worth considering and cost-effective.

3. Reverse Osmosis Water Filter – Best for all types of contamination

Reverse osmosis is one of the water purification processes that uses a semi-permeable membrane to filter out unwanted particles such as sediments, salt, pesticides, nitrates, microbes, heavy metals such as arsenic, lead, and many more from drinking water. Whatever the type of contamination present in your water, reverse osmosis is the efficient system to opt for. 

You can install them under the kitchen sink or over the counter to access clean water. After rain, if your water turns yellow, it may indicate the presence of sediments, iron, manganese, or septic run-off. Hence, we suggest you install a pre-filter (sediment filter) and post-filters (activated carbon filters or ion exchange) to protect the filters and longevity. 

Various reverse osmosis filters are available, which offer multi-filtration, such as APEC ROES-PH75, that work very well after heavy rain. You can easily buy these filters under the range of 300 to 500$.

4. Iron Filter – Best for Ferric and Ferrous Iron

Iron filters are specially designed to remove iron contamination from the well water. You’ll need a complete solution that can successfully manage all these difficulties when choosing an iron filter for well water that needs to address ferric and ferrous iron as well as iron bacteria.

They work by using different oxidizing media such as greensand, oxidative air filter, and aeration media followed by filtration, injecting chemicals such as chlorine or hydrogen peroxide, birm, or manganese dioxide. All the mechanisms work by oxidizing a dissolved iron into solid particles, which can be easily removed using a filter. 

Usually, the yellow water because of ferrous iron is challenging, so you need to oxidize it by using the media mentioned above. Your choice of media selection depends on efficiency and budget. For more detailed info, check out the Cheapest way to remove iron from well water.

You can install them as whole-house iron filters at the point of entry, and you can check our list of our top picks. Lastly, It’s advisable to test the well water before installing them. Additionally, regular maintenance and monitoring of the well and water treatment system will also contribute to reducing iron contamination.

5. Water Softener or Ion Exchange – Best for Minerals and Metals

Water softener works on the mechanism of Ion exchange. It is an incredible choice for high levels of hardness, hence low levels of dissolved iron or ferrous iron (up to 3 ppm). When water flows through the media resin bed, it attracts all the calcium, magnesium, and some of the iron ions, traps and removes them, resulting in no further brown color of your water.

Their availability with the pre-sediment filter is a plus, which removes all the sediments before reaching the ion exchange. Additionally, they can be installed as whole-house water softeners at your water’s point of entry before your water heater to provide water-based appliances with softened hot and cold water.

Importantly, it wouldn’t be good if, other than hardness is your main concern. We’ll suggest using additional filter media in support, such as an activated carbon filter or reverse osmosis. 

6. Replace the Corrosive Plumbings – Best to Prevent Corrosion

If rain has affected your plumbings, well casing, or components, then replacing them with new ones is only the better solution. The untreated components can produce rust flaskes from your tap that eventually lower the water quality and offer more damage to fixtures. If you want to get rid of brown water, it is better to treat it before you need to invest more. 

If you want to prevent corrosion in the future, we suggest using PVC material instead of iron and steel, which is cost-effective. 


It is a good idea to have your well water examined. It’s crucial to comprehend the underlying causes and take action to remedy them. Finding the cause of the problem is essential to developing a workable remedy, regardless of whether the problem is sediment disturbance, bacterial contamination from run-off, or mineral leaching from the soil. 

Your well water may stay safe, clear, and discoloration-free even after a lot of rain with routine testing, good maintenance, and, if necessary, filter or treatment equipment installation.

Scroll to Top