How To Grow Beneficial Bacteria In Ponds (DIY Methods)

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How to Create & Promote Good Bacteria Growth Within Ponds 2022

Several orange koi in a clear pond with lily pads
Bacteria in ponds are responsible for the breakdown of waste substances, which keeps water clear and healthy. Public domain.

Good bacteria, as covered briefly in our article on the types of bacteria and other microorganisms in ponds, are absolutely essential for the survival of virtually all ecosystems as well as the creatures, both flora and fauna, within them (including humans). They aid in the decomposition of organic material and the cycling of nutrients, thereby helping to break things down and, when it comes particularly to aquatic ecosystems, prevent buildup and stagnation in the water.

Similarly, they also cycle ammonia and nitrites before they reach levels that may be toxic to your fish or other wildlife. Specifically, heterotrophic bacteria are the ones responsible for breaking down organic matter, while autotrophic bacteria aid in oxidizing ammonia, nitrites, and sulfides and sulfates  – improving pond water quality.

Is Pond Bacteria Beneficial to Fish & Wildlife?

A white, orange, and black koi in a clear pond with beneficial bacteria
Beneficial bacteria aid wildlife by strengthening their bodily functions, and also improve the slime coating of fish. Public domain.

In addition to the water quality benefits, wildlife that drink water with healthy bacteria species and levels will boost their own systems, the bacteria then aiding their bodies in breaking down food, fighting illnesses and parasites, improving immune system development and function, and overall keeping their/our internal systems running smoothly.

For your fish specifically, beneficial bacteria in the water help to provide a healthy slime layer on your fish and thus prevent illnesses such as ich from being able to establish.

Bacteria will also help prevent algae blooms by competing for the nutrients that algae rely on. Even the dreaded cyanobacteria are good so long as they aren’t allowed to grow out of control – cyanobacteria fix nitrogen so that it is accessible for other organisms, such as plants, to utilize. Bacteria are crucial for clean, healthy water, so much so that most waste water treatment plants utilize bacteria to filter many billions of gallons of water each day, no matter how polluted, making them masters at ensuring our precious freshwater remains a renewable resource.

Ways to Promote Good Pond Bacteria Growth Naturally (Top Methods)

1) Add Natural Healthy Water (Ponds Without Fish)

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Perhaps one of the simplest ways to incorporate beneficial bacteria into your pond is to find a local natural water source (thereby ensuring that the bacteria will be native to the area’s conditions and thus well-suited to your pond), check to make sure overall quality is good, and then take a bucketful or two of the water and dump it into your pond. A single drop of water contains billions of microorganisms, so adding even just a small amount can really help kick start the colonization of good bacteria in your pond.

One potential drawback of this is if there happen to be any parasites or other harmful microorganisms in the water, they will get added to your pond, which is why this method is only recommended for ponds without fish, wildlife ponds or natural water bodies.

How Do You Know If Water Is Healthy?

These natural bacteria need particular water parameters in order to thrive, so check to make sure that the water has a neutral pH somewhere between approximately 6.8 and 7.4, less than 1 part per million (ppm) of ammonia, and less than 5 ppm of nitrates. In this study, it was found that ponds with higher pH and ammonia levels had lower populations of beneficial heterotrophic bacteria, and those with more beneficial bacteria had healthier water quality with more neutral pH and less ammonia and nitrates. Therefore, when using natural water that is within the conditions mentioned above, there’s a high probability that it will contain plenty of beneficial bacteria that you can then add safely to your pond.

2) Provide Plenty of Surface Area

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Depending on the species, bacteria are generally not overly mobile and therefore need some form of surface to settle themselves on. Adding plenty of plants, rocks, substrate, and so on will add to the overall surface area available for bacteria to utilize and colonize.

Studies have found that bacteria establish and multiply much more readily on things that have more surface area as well as things that have rougher textures – for example, they are likely to prefer a rock that is coarse-textured with bumps and pockmarks where they are able to easily attach as opposed to a smooth rock that resultantly has less surface area and is also more difficult to attach to.

3) Afford Ample Aeration

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More dissolved oxygen in water correlates positively with increased primary production, meaning that water with plenty of aeration is better able to host beneficial bacteria because it enables them to be able to properly cycle nutrients and, thus, live.

With this in mind, incorporating air pumps, bubblers, oxygenation plants, and some water movement will all facilitate increased dissolved oxygen levels that enable the establishment and survival of good bacteria.

4) Supplement with Helpful Bacteria Products

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There are bacterial products that are available for purchase from many stores, which contain a plethora of advantageous bacteria that can be added to your pond. Both dry and liquid varieties are available; dry options work best in waters that are above 60° F (15.5° C), and are much more concentrated so these are typically utilized when trying to initially establish and/or promote the growth of healthy bacteria. They often come in pouches that can be simply tossed in the water, and should be placed near some sort of aeration feature to help disperse the bacterial mixture.

Liquid varieties are considered more of a “maintenance” product, helping to keep current bacteria populations healthy, and are typically applied perhaps once a month or as needed, and work in either warm or cool waters. There are hardy varieties available that are suited to cooler water temperatures to help ensure healthy water quality through the winter, as well. Many of these products also contain vitamins for your fish. Regardless of the type of product that you use, be certain to pay close attention to the label and use as directed.

There are also bacteria dispensing solutions available that continually, gradually, and evenly disperse bacteria and enzymes into your pond for up to 30 days. This option may be ideal for those who are forgetful or don’t wish to repeatedly apply products to their pond, as dispensers will do it for you.

Things to Keep in Mind When Growing Pond Bacteria For Best Results

1) Restrict Chemical and Fertilizer Use

A pond with an algae bloom
Fertilizer run-off can cause all sorts of pond issues, including algae blooms, a reduction in bacteria, and poor water quality. Public domain.

As might be expected, chemicals are typically designed to harm something and as such are not only likely to, but will, harm other things as well. Bacteria are small, sensitive organisms, and are easily impacted by chemicals such as herbicides and pesticides that may be applied to ponds. Copper products in particular are known to reduce the efficacy of bacteria. Therefore, only use these products if absolutely necessary, after first exploring any natural options possible for treating whatever issue you may have in your pond, as discussed in many of our articles on pond weeds, algae, and so on.

Similarly, fertilizers also impact bacteria. Though natural, fertilizers are meant to facilitate the growth of plants and are used worldwide on lawns, crops, gardens, and flowerbeds. However, these fertilizers can then settle into the soil and leach into your pond, or runoff into it via watering or rainfall, which will in turn feed the bacteria in your pond…perhaps to unhealthy levels.

Just about anything in too high of a quantity can become harmful, and this is true of even the beneficial species of bacteria. In addition, the excess nutrients from the fertilizers will alter the overall water quality, overload the system, deprive the water of oxygen as it tries to break down the nutrients (thus potentially killing fish, plants, and microorganisms like bacteria), and will feed all manner of algae.

2) Dechlorinate Mains Water

During substantial, heavy water changes, it’s imperative that you dechlorinate the mains water. Chlorine is often used in mains water to deter the growth of bad slime bacteria that could build up in the system, but chlorine is toxic to fish and bacteria alike (and will kill both good and bad bacteria without discrimination). While having a (very) small amount present in the mains water is alright, during heavy water changes you should be sure to dechlorinate the mains to prevent any chlorine from rushing out into your pond and killing off your helpful bacteria or poisoning your fish.

3) Limit Organic Matter

Maple leaves in a pond
Too much organic matter in ponds, like fallen leaves, can deplete oxygen levels, reduce beneficial bacteria, and feed algal growth. Public domain.

While bacteria are adept at breaking down organic matter, having too much of it will result in them not being able to decompose it quickly enough. As a result, your pond will be overloaded with nutrients from the waste and at least some oxygen depletion will occur. Be sure to regularly skim leaves, sticks, and dead insects out of your pond, and if you mow your lawn, do your best to avoid getting grass clippings in the water.

4) Avoid Sudden Water Quality Changes

Some species of bacteria, particularly nitrifying bacteria, are quite sensitive. Therefore, any sudden changes to pH, water temperature, oxygen levels, or sometimes light exposure can kill them, particularly if these changes occur within the first few days of the bacteria being introduced to the pond. If you must make alterations to your pond, do so gradually.

13 thoughts on “How To Grow Beneficial Bacteria In Ponds (DIY Methods)”

    • Hi Sylvia,

      Goldfish and koi both enjoy eating duckweed, so you may consider getting a few of those if you don’t have any already. Another safe way to remove it is to do so manually with a net or pond vacuum, so as to minimize stress to fish or any other critters living in the pond. There are also some natural beneficial bacterial treatments that help to safely kill off duckweed. For more info on duckweed and different ways to control it, feel free to read our article on the topic:

  1. How do I kill or remove small leeches from my small pond? I m a vegetarian, so putting liver etc in cans is out of question. Is there some way I can kill them without harming waterlilies and fishes? Is there an organic liquid etc that can kill them and the eggs?

  2. Thanks a ton for the long and very helpful post.
    I apologise for my late reply.
    My pond is flourishing now, slowly picking up the lost season.The lockdown had added to the woes in maintaining the pond and garden.
    Taking your advice, I added the dwarf scouring rush and a plant looking like a umbrella Palm.
    Everyday worked for about an hour splitting time, and cleaned the muck, algae, filtered the leeches!!
    In about a month and a half, population of leeches had reduced to almost nil, population of fish tripled in 3 months,and lillies are beginning to flower.
    Thanks so much for your help.


  3. This is the first year for that string algae, its clogging up the pump so fast, can you help please,I try to scrape and pull, change filter often..

  4. Im new to ponding but I have a lot of algie, ive started adding salt and the fish have stopped flashing but what can i do about algie im cleaning the pond sbout every 2 weeks and thats a big job , not to mention the stress on my fish
    I have added an all in one filter but still algie and cloudycwsters a problem , please help

    • Hi Gayel,

      Huge apologies for such a delayed reply! We would highly recommend removing as much of the algae as you can with a net, thoroughly cleaning your filter, and adding in beneficial bacteria to help naturally break down the algae. An added bonus is that the beneficial bacteria will not harm your fish, and will naturally multiply, thus increasing their ability to break down algae and other harmful things, like excess food and detritus, as more time goes on.

  5. good morning . I read your article and its was interesting and informative, am seeking information on the use off beneficial bacteria for sea water pond TO GROW SEAWATER FISH IN AQUAPONICS SYSTEM . My question is how can i create this bacteria to make my system reproduce health marine fish.? can i add lime in the system?

  6. Is there any way to get rid of snails? I tried buying assassin snails but never saw them again. I hoped they wouldn’t return the following spring but they are everywhere!! Bog, stream and waterfall rocks!!


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