Learn How to Keep your Pond's Eco-System Balanced for Crystal Clear Pond Water

Posted by Bill Hoffman on May 10th 2021

Learn How to Keep your Pond's Eco-System Balanced for Crystal Clear Pond Water

Keeping your pond’s eco-system balanced can be tricky at times but does not have to be hard.

When you build a water garden, you are not just creating a space for your koi and fish to live. You are creating an eco-system where your pond fish can thrive as well as a community of interacting organisms and their physical environment. You will find that many living creatures will invite themselves in and take up residence - if things are properly balanced.

“If you build it, they will come.”


Pond's Eco-System & its Pond Visitors


Your Pond’s Ecosystem is a balance between fish, plants, bacteria, critters and other living organisms. Think of the ecosystem as a teeter totter, with nutrients (fish waste, plant waste, minerals in new water, fish food, etc.) coming into the pond on one side and on the other side; bacteria, plants filtering out toxins, and nutrients. If nutrients coming into the pond (bigger fish, more waste, fish food) increases, then in order to keep the teeter totter in balance we may need to add a bigger filter, pump or more aquatic plants.


Aquatic Plants: Pond plants are one of the most important, if not the most important part of your pond’s ecosystem and your pond’s filtration. Pond plants are also a hearty food source, lodging, and a great hiding place for bugs, critters and fish. The more circulation of pond water around and through your submerged, marginal and floating plants, the better job of filtering they do. It is also recommended that 40 to 60% of the surface area of the pond be covered or shaded with plant material to help keep water cooler, reduce UV rays from penetrating the water, and give fish some protection from predators.

Different type of Aquatic pond Plants

  • Submerged Aquatics (seaweed or underwater pond plants) are a must for absorbing nutrients and toxic ammonia from the bottom of your pond. They also provide; a place for eggs (as fish spawn), hiding spots for fry, help in controlling water temperatures, and in some cases may even add a little oxygen to the water.
    • One weighted bundle per two sq. ft. of the pond’s surface area is recommended.
  • If your pond’s surface is 8’ x 10’ you will need 40 bundles [Math: 8x10=80 & 80/2=40]
    • As these plants, hornwort for example, absorb nutrients through their leaves, they will grow. They can even be pinched off and re-bundled for added filtration.
  • Water Lilies and Lotus are good plants for providing cover on the pond’s surface. Having a certain amount of coverage will help control water temps and provide security for your pond fish to swim freely around the pond.
    • One plant for every 15-20 sq. ft. is recommended.
    • Water lilies and lotus both offer beautiful colors and textures with its beautiful flowers and leaves.
  • Marginal Plants employ a plethora of job responsibilities. Besides being great filters, they offer beauty, dimension, texture, food, protection, nesting and naturalization to your pond.
    • Marginal pond plants prefer to be in shallower water along the pond’s edges or in a bog filter area.
    • As a general guide on how many marginals should be used, we recommend figuring how many plants it would take to plant approximately 25% of the perimeter of your pond.
    • Marginal pond plants should be utilized as decorative plantings and for filtration. A group of three or five in a bog filter looks great – and can be really beneficial to your water quality!
  • Floating Plants (water hyacinth and water lettuce) are tropical plants. They should not go into pond water until water temperatures are 65 to 70 degrees. Their roots dangle in water from the surface, absorbing suspended nutrients as pond water flows by. Water Hyacinth and water lettuce are fantastic filterers. Its roots also pose as a delightful snack for your finned friends.
    • Floating pond plants reproduce rapidly and will need to be removed and/or relocated as they grow.
    • If you have no more room, they make great compost since they are filled with all that fish waste.
    • Pro Tip: Feeder rings can be used to keep them together in your pond.

Pond Fish: like goldfish, shubunkins, and koi are generally the main residents of most backyard ponds. Keeping them happy and healthy is of utmost importance. It is very difficult to keep pond water clean and healthy in ponds that have too much of a fish load.

  • We recommend adding no more than 1 inch of fish per 2 sq. ft. of surface area during the first year. Remember, fish will grow and multiple so you will want to leave them some growing room. You also do not want to overwhelm the pond filtration system (bacteria that break down fish waste) by adding too many at one time.
    • A well-established pond may be able to handle many more fish - as long as the filtration is adequate.
  • Size matters. Larger fish consume more, create more waste, take up more space, and put a higher demand on dissolved oxygen in the pond.
  • Do not over feed your finned friends. There are many things in the pond for your fish to eat, such as insects, plankton, string algae and hopefully not, but sometimes pond plants.
    • BUT feeding your finned friends can be fun and a bonding experience. They can actually be trained to eat right out of your hand. However, over-feeding is just as dangerous as over-stocking.
    • Fish should only be fed when spring, summer and fall water temperatures are consistently above 50 degrees and below 80 degrees.
      • Water below 50 degrees slows down fish metabolism.
      • Water 80 degrees or more does not hold as much dissolved oxygen and fish waste build up can become toxic - even if you have good filtration.
      • We recommend feeding your fish once a day, what they will eat completely, in 3 to 5 minutes.
        • Or, if you want to feed them 2-3 times a day – give them only what they will eat in 1-2 minutes.
      • Leaving uneaten food in the pond, or skimmer, will decay and cause algae problems and potentially lead to other health issues for fish.
        • Using a feeder ring will make it easy for you to remove uneaten food.
      • The quality of your pond fish food will also have an effect on the clarity of your water.

Fish Waste: Pond fish consume plant and bug life every day, in addition to the fish food that you provide them. In one end and out the other means it all ends up in the bottom of your pond.

  • Plant debris and fish waste are represented as ammonia as they begin to decompose.
    • Ammonia is heavier than water and will settle at the bottom.
      (This is why samples for water testing needs to be collected from as deep as you can reach.)
      • Ammonia can burn fish’s gills, the way smoke from a house fire can burn your lungs.
        • Ammonia starts to harm fish at 0.25 ppm or less. Fish will isolate themselves, become lethargic, clamp their fins, gasp for air at the surface and are much more susceptible to parasites and bacterial infections.
      • Aerator systems and pond pumps will help stir up ammonia to get it to your biological filter - where the beneficial bacteria can break it down.
      • Pond plants will consume broken down ammonia – helping to clean your pond water.
  • Muck build-up comes from decomposed plant material, fish waste, soil and muck runoff, and dead algae.
    • The decomposition process uses oxygen from the pond water.
    • A high demand for dissolved oxygen can lead to your fish gasping for air up at the surface.
    • In warmer water, above 75 degrees, oxygen is found mostly at the surface – unless an aerator is used.
    • Lack of oxygen at the bottom of the pond causes muck to build up and then wait for oxygen it needs to decompose.
      • This lack of oxygen allows anaerobic bacteria to grow - which can lead to infections in your pond fish.
    • Installing a pond aeration system will help greatly with breaking down solids and dispersing them to the proper filters.
  • Mechanical pond filters work by trapping and removing debris (like leaves, mulch, fish waste, etc.) suspended in the pond water. A pond skimmer is the perfect example.
    • Cleaning your skimmer filters will remove suspended waste from the water. It’s like vacuuming your carpets; the more often you do it, the cleaner it will be. **We recommend at least once a week.
  • String Algae is a common sign of having too much waste or too many nutrients in your pond. It will often appear when a biological pond filter is too small, non-existent, or the pH is too high (9+).
    • String algae feeds off of ammonia in the water. This is why, sometimes, we see it wrapped up in the hornwort (seaweed) at the bottom of the pond. These two plant types (hornwort and string algae) are actually competing for nutrients.

Beneficial Bacteria: There are many different types, or strains, of bacteria and enzymes which all have different jobs to perform. The long-term benefit is that beneficial bacteria turn the harmful pond waste into useful plant nutrients.

  • Powdered (dry) bacteria blends, like Pond Basics Pond Starter Dry Bacteriahave multiple strains and cover a wide range of beneficial bacteria and enzymes to handle waste in your pond.
    • Dry blends are dormant in the container and “wake up” once in the water and conditions are just right.
    • This will allow you to add it into your pond early and not have to predict the timing of perfect conditions.
  • Liquid bacteria, such as Microbe-Lift’s PL and Nite-Out II, are live strands in the bottle. Therefore, they will go to work as soon as you put them in the pond.
    • Each one is a different strain and will do its job accordingly.
    • Cold water will affect the effectiveness and could kill them if it is too cold.
  • Your waterfall box can be turned into a biological pond filter by filling it with filter media bags full of Bio-Cubes.
    • As solid waste from the pond is collected in the filter media, beneficial bacteria will colonize and start breaking down (oxidizing) the ammonia.
    • This filter should not be disturbed during the warm season.
  • Circulation is important for moving pond water and any solids through the necessary pond filter. This is not the same thing as having a pond aeration system in place. However, it will share similar tasks at times.
  • Oxygenation is mentioned above under the sub-title waste, but it is also important in the bacteria process.
    • Since beneficial bacteria helps in the decomposition process, oxygen in the water is being used.
    • Running your waterfall 24/7 in the spring, summer and fall will help keep your biological pond filter healthy and oxygenated.
  • Nitrites are the first by-product in the breakdown (oxidization) of ammonia by the good bacteria.
    • Nitrites are less toxic than ammonia, but may still pose a problem over a longer period of time.
    • High amounts of nitrites in the water pass through the gills of fish and over time can cause “brown blood disease.” This is due to a lack of oxygen in their blood.
    • Nitrites become toxic at 1 ppm.


Nitrates are the last chemicals produced in the nitrification cycle, which are the useful nutrients for your pond plants.

  • Nitrates are relatively nontoxic when being compared to ammonia and nitrites, but can still kill fish at very high levels.
  • Nitrates become toxic over 80 ppm.
  • In most ponds, nitrates are usually consumed by algae and aquatic plants well before they kill fish.
    • Lack of pond plants, with high amounts of nitrates, will generally cause green water problems. For more details, please read “Algae Solutions.”

Pond Plants: Nutrients and nitrates are absorbed by pond plants and thus removed from the water.


Now the cycle is complete and begins again!


A Pond's Nitrogen Cycle

**Remember, a pond’s eco-system is ever changing, with fish growth, plant growth, weather conditions, etc. What works for you this year may be different next year. Be patient and do not get discouraged when it comes to your pond. When in doubt, visit the pond experts at Hoffman’s Water X Scapes and we can help troubleshoot any water feature problems with you, like green water and algae issues, and help find a solution that will work for you and your pond.