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Best Toilet Cleaners for Septic Tanks of 2022

Toilet cleaners that won’t damage your septic tank.

Are you worried about your toilet cleaner damaging your septic tank? We had the same issue when searching for a suitable product.

Worry no more, though. Septic tanks and toilet cleaners are nasty business. So we’ve put the hard yards in for you on which product to choose. We’ve also gathered some precious industry insights to help you find the best toilet cleaners for septic tanks.

If you choose a safe product and follow the right cleaning steps, you’ll be able to have a spotless toilet bowl and seat while keeping your septic tank healthy.

Our Top Picks

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Product Comparison Table

Product Image of the Clorox Toilet Bowl Cleaner With Bleach Variety Pack - (package May Vary), 24 Fl Oz (Pack of 4)
Best Stain Remover
Clorox Toilet Bowl Cleaner
  • Eliminates most bacteria
  • Removes hard stains
  • Gentle formula
Product Image of the Church And Dwight 35113' kaboom Scrub Free Toilet Cleaning System (Pack of 2)
Best Hands-Free Cleaner
Kaboom Continuous Clean
  • Easy installation and usage
  • Effective
  • Great value for money
Product Image of the Lysol Clean & Fresh Toilet Bowl Cleaner, Ocean Fresh, 24 oz (Pack of 4)
Best for Deep Cleaning
Lysol Clean & Fresh
  • For deep cleaning
  • Great scent
  • Effective germ removal
Best Natural Cleaning Formula
Green Works Cleaner
  • Safe for septic tanks
  • Natural ingredients
  • Environmentally friendly
Product Image of the Better Life Natural Tub and Tile Cleaner, Tea Tree and Eucalyptus, 32 Fl Oz (Pack of 2)
Best Thick Formula
Better Life Natural
  • Product of U.S.A
  • Biodegradable
  • Effective cleaner

Product Reviews

We’ve spent a good few hours wading through a plethora of toilet cleaners to find the best on the market. After applying the factors above, checking customer reviews and consulting industry experts, we’ve concluded on the list below. These are the best toilet cleaners for septic tanks:

1. Clorox Toilet Bowl Cleaner with Bleach

Best Stain Remover

If you have limited energy for scrubbing toilets, a not-so-effective cleaner won’t work. So, if you’re looking for a toilet cleaner with a formula perfect for deep cleaning your toilet bowl, this could be it.

This toilet cleaner will leave your toilet shiny and new, as it removes all tough stains and bowl rings. Since it contains bleach, it also eliminates most odor-causing bacteria. For messier toilet situations, apply it overnight and you’ll wake up to a bacteria-free situation.

This Clorox formula is non-abrasive, and according to the company, is safe to be used in septic systems. Regardless, though, we advise you to be careful while using this toilet cleaner. It contains some toxic materials.

If your house has a septic tank, we recommend you use it sparingly. Always use gloves and be careful not to splash eyes or clothing.


  • Eliminates most bacteria.
  • Removes hard stains.


  • Toxic ingredients.

Product Specs

Size 24 ounces
Bleach Yes
Scents Cool Wave, Fresh
Safe for septic tanks? Yes

2. Kaboom Scrub Free! Toilet Bowl Cleaner

Best Hands-Free Cleaner

If you’re a busy mom who has limited time to do the cleaning and despises the stinky odor and toilet grimes, you’ll absolutely love this toilet cleaner from Kaboom.

It’s an innovative toilet cleaning system that continuously cleans and deodorizes your toilet bowl. It requires less than a minute of installation and gives you several months of hands-free cleaning. Because this cleaner needs to be directly installed to your overflow pipe, it perfectly cleans not only the toilet bowl but also underneath its rim and the water as a whole. It’s safe for septic tanks too.

It removes tough stains and deposits well, leaving behind a fresh scent.


  • Easy installation and usage.
  • Effective.
  • Great value for money.


  • Not compatible with all toilet design.

Product Specs

Size 6.4 ounces
Bleach Yes
Scents Slight scent of bleach
Safe for septic tanks? Yes

3. Lysol Clean & Fresh Toilet Bowl Clean

Best For Deep Cleaning

This Lysol toilet bowl cleaner is one of the most loved on the market. For anyone who wants to do a toilet deep clean, this could be the perfect cleaner.

With this product, it’s very easy to remove toilet rings, hard-water stains and rust. In extreme cases, you’ll just need to use the toilet scrub to easily make them go away. The bottle is perfect for hard-to-reach areas, making it easy to clean under the rim.

It contains bleach, which means it’ll effectively remove most germs from your toilet. This product is also pretty thick, clinging to the toilet while disinfecting it. As such, you just need to squirt some gel into the toilet and leave it for a few minutes before flushing.

You can also use it to clean other hard surfaces, such as your electronic devices. Finally, you can choose between three different scent options. Each of these leave behind an amazing fresh and clean smell:

  • Lemon and lime.
  • Crisp linen.
  • Early morning breeze.


  • Perfect for deep cleaning.
  • Removes difficult stains.
  • Effective germ removal.


  • Tricky bottle opening.

Product Specs

Size 24 ounces
Bleach Yes
Scents Lemon and lime, crisp linen, early morning breeze
Safe for septic tanks? Yes

4. Green Works Toilet Bowl Cleaner

Best Natural Cleaning Formula

This toilet bowl cleaner has a powerful cleaning formula that leaves the bowl smelling fresh. It removes even the most tricky stains, rust, hard water stains, and mineral deposits.

For the environmentally friendly among you, this product combines naturally derived and plant-based ingredients, cleaning any dirt present in the toilet bowl efficiently. The packaging is made of recycled or post-consumer plastic. Its contents are also cruelty-free since they’re not tested on animals.

Not containing bleach, it doesn’t kill the good bacteria needed for a balanced septic system. It also doesn’t create harsh chemical fumes or residue while you’re cleaning.

With the angled spout, it reaches hard-to-get areas under the rim, cleaning them appropriately. To wash off the trickier hard water stains, you can use a brush to scrub the stubborn areas.


  • Safe for septic tanks.
  • Natural ingredients.
  • Environmentally friendly.


  • Hard stains require scrubbing.

Product Specs

Size 24 ounces
Bleach No
Scents Original Fresh
Safe for septic tanks? Yes

5. Better Life Natural Tub and Tile Cleaner

Best Thick Formula

If you’re looking for something natural, this cleaner might be a great option. It makes toilet cleaning a not-so-nasty chore, making tough stains go away easily.

The thick gel sticks to the toilet walls, cutting through grime, rust and calcium deposits. It also removes rings and dirt buildup, making your household chores easier.

This Better Life cleaner is made of plant-derived products. More still, it’s free of dyes, sulfates, petroleum solvents and synthetic fragrances. It’s also safe for septic systems and waterways, which makes for an eco-friendly product.

Also, all ingredients are biodegradable, not tested on animals, and its packaging is made of recyclable materials.


  • Eco-friendly product.
  • Safe for septic systems and waterways.
  • Effective cleaner.


  • Overbearing and chemical smell.

Product Specs

Size 32 ounces
Bleach No
Scents Tea tree and eucalyptus
Safe for septic tanks? Yes

Product Comparison Chart

Product Best Size Bleach Scents
Clorox Toilet Bowl Cleaner Stain Remover 24 oz Yes Cool Wave, Fresh
Kaboom Scrub Free! Toilet Cleaner Hands-Free 6.4 oz Yes Slight bleach scent
Lysol Clean & Fresh Toilet Cleaner Deep Cleaning 24 oz Yes Lemon & lime, crisp linen, early morning breeze
Green Works Toilet Cleaner Natural Formula 24 oz No Original Fresh
Better Life Natural Cleaner Thick Formula 24 oz No Tea tree and peppermint

How to Choose a Septic Tank Cleaner

It’s vital that you don’t just grab a random product off the shelf. Toilet cleaners are designed to lure you in with flashy words and clever marketing. Instead, consider these points when choosing a product:

Avoid Cleaners With Harsh Chemicals

Many toilet cleaners contain harsh chemicals. The two most common are bleach and hydrochloric acid, which in large quantities, can be harmful to septic tanks. These chemicals reduce or eliminate “healthy” bacteria that septic systems need to work properly (1).

You should also beware of cleaners containing ammonia, phosphates or solvents. These also kill the “good bacteria” necessary for your septic system to work properly.

Be Careful

Septic systems can’t filter many solvent-based products or disinfectants in large doses. Just 1.85 gallons of chlorine bleach within a short period can kill most of the bacteria needed for a healthy 1,000-gallon septic tank. (2)

If you do decide on using a toilet cleaner containing harsh-chemicals, make sure you’re protected. Use gloves, eye protection and appropriate clothing while cleaning. Some toilet cleaning products can cause skin burns or damage to your eyes. (3)

Also, remove carpets and other household items around the toilet. This ensures you don’t ruin them if they come in contact with the products.

Natural Toilet Cleaners Are a Great Option

On the opposite end of the spectrum, you can use natural cleaners like white vinegar, baking soda or lemon juice.

And, if you have time and are a DIY fan, you can always create your toilet cleaner. Some recipes also include alcohol, citric acid, oils or dried up spices.

It’s a very affordable, non-toxic and eco-friendly option, which can clean, disinfect and deodorize your toilet.

Choose Efficient, Green Toilet Cleaners

If you’re looking for efficient cleaning while staying eco-friendly, you can use safe and mild toilet cleaners. These do a better job cleaning and killing bacteria.

Check for products labeled non-toxic, biodegradable and environmentally-friendly. These will prevent you from harming your septic tank, polluting underground water or exposing you and your family to harsh substances.

According to the United States Environmental Protection Agency, the safest choice is to use “green” cleaners that don’t contain petroleum-based solvents. You can even check on their website if the product you’re buying is an eco-friendly choice (4).


How to Clean a Toilet Properly

  1. Clear the area: Remove items from around the toilet and tank lid.
  2. Apply the cleaner: Flush the toilet and then apply the cleaning product, letting it sit for at least 5 minutes.
  3. Clean the exterior: Start at the top, to prevent dirt from dripping on clean areas.
  4. Mop the floor: The floor around the toilet should be cleaned at this stage.
  5. Clean the toilet seat: After raising the toilet seat, spray the inside lid and rim with cleaner.
  6. Wipe the toilet seat: Use a moistened cloth with clean water.
  7. Clean the toilet bowl: Do it from the top down.
  8. Scrub the drain hole opening: Scrub well and flush the toilet with the lid down.
  9. Spray the walls: Do this behind and beside the toilet.

How to Remove Rust and Mineral Stains

  1. Flush and scrub: Flush the toilet and scrub the affected areas with baking soda or your preferred anti-rust remover.
  2. Alternative options: You can also pour a can of cola in or some vinegar to dissolve the trickiest stains.
  3. Flush: Finish by flushing the toilet with the lid down to prevent splashing.

What Cleaning Supplies Do I Need?

  • Rubber gloves.
  • Toilet brush.
  • Eye protection.
  • Liquid toilet cleaner.
  • Spray cleaner.
  • Paper towels or cloths.

How Can I Be Safe While Cleaning a Toilet?

  • Wear protection: Protect your eyes from bleach and chemicals by wearing eye protection.
  • Seat down: Whenever you flush the toilet, keep the seat down.
  • No sponges: Avoid using sponges as these easily breed bacteria.

Protect That Septic Tank

Not all products on the market may be a safe option. If your house has a septic system, stay clear of those with harsh chemicals. A biodegradable, naturally-ingredient toilet cleaner will help you remove stains and odors while keeping your septic tank healthy.

It’s important to check the ingredients, and as you can see from our list, plant-based and natural ingredients are best. If you do decide on cleaners containing bleach or other chemicals, it’s essential that you use them modestly.

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Headshot of Sylvia Jones

About the Author

Sylvia Jones

Sylvia Jones is a hands-on, DIY aficionado from Indiana. She is passionate about home improvement, gardening, and environmental conservation. In her spare time, you can find Sylvia getting involved in home improvement projects around the house with her husband, or spending quality time out in the yard.