Best Toilet Cleaners for Septic System Tanks (Septic-Safe Cleaning)

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If you have a septic system on your property as we do, you’re probably looking for cleaning products that are septic-safe.

Harsh, toxic chemicals can actually kill the “healthy bacteria” that thrive inside your septic system and naturally break down the waste inside the tank. Many commercial toilet bowl cleaners contain bleach and some even are made with hydrochloric acid.

While the acid does effectively dissolve the calcium carbonate deposits in the water it’s also a harmful chemical that can contaminate well water and kill off the bacteria in your septic system. 

Some experts have confirmed that a modest amount of chlorine bleach will kill off the good bacteria in your tank. However, in the marketing of Clorox® Toilet Bowl Cleaner and other products the company claims that bleach is safe to use in septic systems.

With all this confusing marketing it’s hard for consumers to really know what products to buy that will actually clean their bathroom but at the same time not do harm to the natural balance of their waste disposal systems.

The best toilet cleaners for septic tanks are ones made from natural and plant-based ingredients since they are biodegradable and use cleaning agents that easily break down (which is why we also recommend using septic-safe laundry detergent).

You can make your own cleaner at home just as my grandmother did with a few simple and natural ingredients, many of which you may already have around the house. You can scroll to the end of the article or click here to skip to the ingredients and steps for making it.

If you’re in a hurry, here are our top picks:

If you don’t want to bother making your own cleaning products, there are several commercial products available that are plant-based and safe to use, like this Toilet Bowl Cleaner by Eco-Me.

If you’re not a fan of peppermint scent, you may prefer the pine-fresh scent of this Ecover Toilet Cleaner.

All of the toilet cleaners on our list below are plant-based and biodegradable. None of the cleaners on our list contain and bleach, ammonia, phosphates or petroleum-based chemicals. They all rate highly on 3rd party environmental safety tests. 

Here are a few recommended products to consider using if you have a septic tank system:

Best Septic-Safe Toilet Bowl Cleaners

Ecover Toilet Cleaner:

Ecover Toilet Bowl Cleaner, Pine Fresh, 25 Ounce
Ecover Toilet Bowl Cleaner (Image: Amazon)

This toilet bowl cleaner from Ecover removes tough stains while de-calcifying and freshening the toilet. It is powerful and hygienic while being eco-friendly. The reasons why it is suitable for use with a septic system are that it is produced with plant-based ingredients, it is easily biodegraded, it has a very low impact on aquatic life.

The ingredients in this cleaner, including the surfactants (the active ingredient that does the actual cleaning), are all plant-based which makes it a safe choice for your septic system tank.

Ecover’s packaging is also friendly to the environment. The bottles are 75% Plantplastic® and 25% post-consumer recycled plastic (PCR). Plantplastic® is a proprietary plant-sourced plastic made from sustainably harvested sugarcane. Ecover cleaning products are not tested on animals.

The bottle is completely recyclable and can be recycled in most city curbside recycling programs along with your other containers and newspapers. This makes the Ecover Toilet Cleaner very suitable for use with a septic system.

Eco-Me Natural Powerful Toilet Bowl Cleaner

Eco Me Natural Powerful Deep Cleaning Toilet Bowl Cleaner, Healthy Herbal Mint Scent, 32 Ounces
Eco-Me Natural Toilet Bowl Cleaner (Image: Amazon)

Eco-me is a family business that was founded in 2006 when the founder’s sister was diagnosed with breast cancer at the young age of 35. This set the family off on a mission to create a line of cleaning products that were safe to use while still cleaning the house as good or better than the harsh chemicals that fill the cleaning cupboard.

The result of their research and effort is this septic-safe toilet cleaner. It has a pleasant mint scent and comes in a convenient 32-ounce bottle.

All of the Eco-Me products are made following the Natural Products Association (NPA) guidelines and do NOT use any of the following chemicals.:

  • No Petro-Chemicals
  • No Sulfates
  • No Synthetic Fragrances
  • No Colorants or Harmful Preservatives

Eco-me products use plant-based and food grade. All of their products are made in the USA.  They have been rated FOOD-GRADE & PLANT-BASED INGREDIENTS * STEAM DISTILLED PLANT ESSENTIAL OILS
Rated #1 by Whole Foods Eco Scale for premium ingredients. Top rated by

Eco-me Toilet Cleaner Ingredients: Water, Coco Glucoside (Plant-derived soap), Decyl Glucoside (Plant-derived Soap), Capryl Capryl Glucoside (Plant-derived Solubilizer), Leuconostoc (Radish Root Antimicrobial), Xanthan Gum, Natural Plant Essential Oils, Glyceryl Caprylate Caprate (Vegetable-derived Thickener), Potassium Sorbate (Food-grade Preservative)

The one main complaint that would prevent us from recommending this toilet cleaner is if you dislike or have an allergy to mint (or peppermint).  Many people find the scent rather strong, while it’s pleasing and “fresh-smelling” others may find it overpowering. If you do not like the smell of mint this is not the product for you, go with the pine-scented Ecover (reviewed above) or maybe the next one on the list (Green Works) that has a fresh spring fragrance.

Mrs. Meyer’s Lemon Verbena Liquid Toilet Bowl Cleaner

Mrs Meyer Clean Day Septic Safe Toilet Cleaner
Mrs Meyer Clean Day Septic Safe Toilet Cleaner

From one of our favorite cleaning brands,  Mrs. Meyer’s, comes this biodegradable toilet cleaner with no phthalates, chlorine, or harsh mineral acids

The cleaner is made with essential oils and plant-derived chemicals with a pleasant scent of Lemon Verbena. The scent comes from the mixture of natural oils used including Lemon Peel Oil, Fir Leaf Oil (Abies Alba and Lemongrass Oil.

Mrs. Meyer’s cleaning products are also cruelty-free and come with the  “Leaping Bunny Certified”, giving you the added benefit of knowing that none of their products are tested on animals.

Green Works Toilet Bowl Cleaner:

Green Works Toilet Bowl Cleaner, Toilet Gel Cleaner - 24 Ounces
Green Works Toilet Bowl Cleaner (Image: Amazon)

The Green Works Toilet Bowl Cleaner is a cleaner that gives a powerful cleaning performance coupled with the fact that it is made with naturally derived and plant-based ingredients, which is one of the reasons it is quite ideal for use with a septic system.

It is very effective at cleaning that cuts through the most stubborn stains. This powerful formula is known to remove rust, mineral deposits, and hard water stains without leaving any residue or harsh chemical fumes.

Once applied to the toilet bowl, the thick gel coats the entire bowl like a nylon cover and starts its action by cutting right through the dirt and leaving the toilet fresh and clean. Its angles spout is designed so as to reach places like underneath the rim making it easier to clean. The cleaner does not contain chlorine bleach and stills clean extremely well.

Greenworks is made by the Clorox company so if you are used to using their products, this is their non-chlorine and non-toxic toilet cleaning option that consists of 99% all-natural ingredients.

Several readers have asked If Comet cleaning power is safe to use with a septic system? (click to find out what we discovered).

Seventh Generation Toilet Bowl Cleaner

Seventh Generation Emerald Cypress and Fir Scent Toilet Bowl Cleaner 32 oz, 8-Pack
Seventh Generation Toilet Bowl Cleaner (Image: Amazon)

This natural toilet bowl cleaner comes in a pleasant Emerald Cypress and Fir Scent: the Seventh Generation Toilet Bowl Cleaner is made with a formula that consists mainly of plant ingredients that attack stubborn stains found on the toilet bowl and leaves it sparkly clean in a flash.

The Emerald Cypress and Fir Scent is made totally from essential oils and botanical extracts, which make it suitable for use with a septic system while maintaining its powerful cleaning action with a pleasant smell. It cleans effectively without producing harsh residue fumes that are toxic to health. It is biodegradable and septic-safe.

It does not contain chlorine bleach nor synthetic fragrances and dyes that might be harsh to both the user and the toilet bowl. And as expected with products by Seventh Generation, the company uses sustainable production to minimize the impact on the environment.

Its flip cap is designed so as to effectively reach spots that are hard to reach like up under the toilet bowl rim.

The cleaner is a very effective, non-chlorine, non-toxic, biodegradable cleaning product that is safe for use with a septic system.

Better Life Natural Toilet Bowl Cleaner

Better Life Natural Toilet Bowl Cleaner, 24 Ounces, 24212
Better Life Natural Toilet Bowl Cleaner (Image: Amazon)

This plant-based toilet bowl cleaner by Better Life is designed to be squirted under the rim and left for 5-10 minutes before brushing and then flushing the toilet to rinse. The product is free from the following chemicals making it a safe option for your septic system and for maintaining a toxic-free home in general.

As mentioned with the Eco-me, the one issue with this cleaner may be the fragrance (Tea Tree and Peppermint). If you don’t like the minty smell, you may want to go with the Green Work “fresh scent”.

  • Chlorine
  • Synthetic fragrances
  • Bleach
  • Dyes
  • Petroleum solvents
  • Phosphates
  • Ammonia
  • Sulfates
  • Petrochemical solvents

The Better Life company was founded by two dads that wanted to make safe cleaning supplies for a toxic-free home. You may be familiar with the company already as millions saw them on Shark Tank when they pitched their cleaning supply company. The pitch ended with a somewhat shocking effect where one of the founders (Kevin Tibbs), sprayed their What-EVER! all-purpose cleaner into his mouth!

The stunt (and the products) convinced the judges and they ended up landing a huge deal with one of the “sharks”. Since then the company has had huge growth and now sells a wide variety of household cleaning supplies that are non-toxic and also septic safe. A scene from Shark Tank.

cleaning toilet bowl
Plant-based toilet bowl cleaners are the best option for septic systems.

DIY Septic Safe Toilet Cleaner

Here is the easiest cleaner I know how to make that actually works:

Mix the two ingredients in a spray bottle, when you blend them – spray the inside of the bowl and even the outside, lid and tank and handle. Wait for several minutes before scrubbing the entire inside of the bowl with a toilet brush and wiping down all surfaces with a clean cloth.

Optional:  After spaying the solution, sprinkle a small amount of baking soda on the inside of the bowl. The soda and vinegar will mix and froth on contact and that bubbling action may help break up minor mineral build-up. As with any DIY cleaner – you’ll most likely need to put in a little extra elbow grease compared to harsher chemicals that do some of the work for you.


  • Never add vinegar to chlorine bleach; the combination creates a deadly mix- noxious chlorine gas.
  • Use new spray bottles. Never re-use spray bottles from cleaning products. There could be traces of chemicals that could mix with the vinegar.
  • The initial smell of the mixed vinegar and concentrated oil can be overpowering especially if stirred or shaken -mix in an open area with proper ventilation.
  • It is important that you use vinegar and essential oils carefully, both can irritate your eyes.

If you’ve never used tea tree oil for household cleaning, here are some of the reasons to start.

More Cleaning Tips For Septic Systems

Here are a few things to consider when purchasing a toilet bowl cleaner, and bathroom cleaning supplies in general, if you have a septic system.

As we mentioned in our article about how a septic system works, in a properly functioning system, the tank needs to have a healthy balance of bacteria to break down the solids inside the tank.

Large amounts of harsh chemicals can upset the balance of the tank and kill off the “good bacteria” that are working to process your household waste. Therefore it’s recommended that whenever possible you use bio-degradable cleaning products and avoid ammonia, anti-bacterial and chlorine-based products.  

While we do not use any enzymes, many people do use them to maintain the healthy balance of bacteria in their septic tank, you can also see how to make an easy DIY septic system activator here. 


no toxic label from cleaning products

Purchasing the right toilet cleaner that does not have negative impacts on the septic system is not difficult. All the user has to consider is its ingredient to determine whether it is biodegradable or not.

Toilet cleaners made from plant materials are usually the ideal cleaners that are suitable for septic systems because they are non-toxic and easily biodegradable. In the long run, these will help maintain the balance in your tank and make it work more efficiently lessening the frequency that you have to get it pumped.


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