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How To Clean Pond Water With Fish In It: Step By Step Guide

Top view of a pond with plants and fish in it.

Having a pond with fish is one of the most fun things you can have in your garden, especially when the water is clear and you can see them swimming around. But when algae and other problems start appearing, you need to find a way to fix the pond water without removing the fish.

Here are the basic steps:

  • skim the water surface
  • remove plants
  • remove pumps
  • remove decorations
  • slowly clean the bottom of the pond with a net
  • remove about 90% of the algae growing on the pond surface
  • clean the pump and filters,
  • once clean, put everything back

You need to consider several things when cleaning a pond, especially to keep the fish in the pond. Many people take too long while cleaning or get too aggressive, causing the pond water to become so murky it is nearly impossible to properly clean.

What Are The Steps To Cleaning Pong Water With Fish In The Pond?

Now that we have the basic steps down, we will take a look at the exact steps required to get your pond as clean as possible. You should rarely need to add chemicals to the water if you want to keep the entire pond clean and the water fresh.

Most people only add chemicals to the water when they notice that the fish are unhealthy and the water has a big imbalance. Instead, you need to get the steps right and repeat them at least once a month to keep the water clear and sparkling.

  1. Skimming: Skimming should be done at least twice a week to ensure that no dead leaves or animals sink to the bottom. Your fish will also appreciate it; it is the first step for the pond water to be as clean as possible for the fish.
  2. Removal: Next, remove all the filters, decorations, and pumps from the pond. This will ensure they don’t get damaged, and allow you to clean around them in later steps.
  3. Cleaning Surfaces: Using a pond skimmer and not a pool broom, scoop everything on the bottom of the pond floor up. This can be sediment, algae, or just dead biomass; you can also use an external pump to suck all of this up if you have the budget.
  4. Removing Algae: Algae is usually the reason any pond turns brown or green, and it needs to be removed throughout your pond. Remove the clumps of algae growing along the sides, leaving some fish to enjoy some algae in the water.
  5. Clean Filters: The free-floating algae that are causing murkiness in your pond water should be removed by the pond filters. Cleaning these filters once a week with tap water is usually a good way to keep the pond clear, do so before replacing everything you removed from the pond.
  6. Replace Everything: Now that the pond is clean and your fish have thoroughly given you the side-eye, you can start replacing everything. The decorations, the filters, and the pumps should all go back where they should be, helping keep the fish happy and the pond clear.

What Are The Requirements To Clean Pond Water With Fish?

Now that you know the basic steps needed to clean your pond while your fish are still in it, we need to look at how to keep the pond clear. First-time pond owners might not realize that constant maintenance and hard work are needed to keep a pond clear.

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However, this is not true for most ponds or even pools; you will need to constantly check the levels and the health of the fish. Doing so will ensure that the pond stays clean for much longer; we have several recommendations to ensure that your pond will not become a nightmare to maintain.

A close up of a pond with fish that are orange, dark orange, and white.
Keep a healthy balance of fish

#1: Healthy Fish Population

The biggest and best way to keep a pond clean and clear is to have a fish population that fits your pond size and filtering capabilities. This is important as a pond with too many fish may quickly become so filled with fish waste that nothing can keep the water clean and clear.

Further, if there are not enough fish in the pond or you have the wrong fish combinations, the pond will become harder to maintain properly. We recommend checking on the fish regularly, ensuring there are enough and that they are all healthy enough to keep the water clean.

#2: Don’t Over Feed

Any food you are giving to the fish that isn’t eaten will naturally cause the pond to grow more algae. Further, any uneaten food may also attract unwanted critters near or in the pond, causing more waste and straining the filtration systems of the pond.

NOTE: The feed breaks down and takes a long time to filter out of the water. Overfeeding causes a thick layer of sediment, creating the perfect place for other things to grow in the pond.

#3: Create A Balance Of Plants

We have seen many people only use artificial plants in their ponds, or use so many plants that nothing else can live in the water. Getting the right balance of natural plants in a pond is important to keep everything clean and level.

The right mixture of water plants and plants on the pond’s edge will naturally filter the water and add much more oxygen. Many fish types specifically prefer to live and hide under plant leaves, which means that you need to keep the balance right and ensure the plants are healthy.

#4: Get The Right Sized Pump

The small pump you would use for an indoor aquarium does not work with an outdoor pond that is easily five times the size. You need to get the right pump size for your pond, larger pumps like this one from Amazon are generally the safer bet to choose from rather than the smallest pump you can find.

We always recommend that people consider that a fountain needs more power when designing and building a pond. If you have a pump that can empty the pond with ease, it should be strong enough to do everything needed.

Top view of a green murky pond with lots of fish, and debris floating on top.
Leaves and debris need to be cleaned regularly

#5: Clean Debris Often

The pond surface will get littered with sand and leaves, maybe even plastic waste if it is windy outside. Further, during autumn and winter, the number of leaves in the pool will drastically increase each day as the leaves from nearby plants fall into the pond.

Cleaning debris once or twice a week should keep most of it from settling at the bottom of the pond, and everything will be fine. However, we also recommend that you clean the pond whenever you see something causing an unreasonable amount of debris.

#6: Get A Filtration System

The biggest problem with first-time pond owners is that they do not realize that ponds need filtration systems. While these systems do not need to be as strong or complex as a pool, they still need to keep the pond water as clean and clear as possible.

Getting even just a small filtration system will ensure that the pond stays clean, giving you the chance to relax a bit more. However, we recommend keeping an eye on the filtration system as it will need to be rinsed and cleaned every few weeks to ensure the algae isn’t overpowering it.

#7: Keep The Pond Cool On Hot Days

The warmer the water is, the more algae will grow in the pond, so keep the pond cool on hot days. Sometimes this can be done by:

  • adding and removing water regularly
  • using tap water
  • using stored water from a larger body of water

However, the best way to keep the pond water temperature in check is to have as many plants as possible covering it with leaves. The fish and the plants enjoy the natural shade while ensuring that the pond can self-regulate the total temperature of the water.

How Do You Clean Pond Water Without Harming Fish?

The most important thing to remember is that you cannot just add any chemical when the fish still live in the pond water. This means that you need to manually clean the water, removing anything that may be a problem or causing the water to be dirty.

However, if you have a pond that is several hundred square feet, you can use dyes like this one from Amazon, to color the water. This kills off the algae causing the water to be dirty.

NOTE: This only works only as a temporary solution and the algae will begin growing again.

If you want to consistently keep the pond as clear as possible, you need a strong filtration system that removes the excess algae growth. Whether this is a pump system or a series of algae-eating fish is entirely up to you and how you want to keep your pond alive.

A pond with a thriving amount of plant life in it and surrounding it.
Plants are a great way to keep a pond clean

How Do You Make Pond Water Clear Naturally?

There are many ways to naturally keep pond water clear, but one of the most successful ways that have recently gained popularity is to use plants. When plants filter the water through their roots, the water can become naturally kept clear without too much of a problem.

NOTE: To learn more about adding plants to your pond, read my article about the best time to plant pond plants!

Further, keeping the fish populations in check will help keep your pond as clear as possible, allowing you to do less hands-on maintenance. Ensure your pond water stays clear by getting the right combination of:

  • natural filtration systems
  • fish that eat algae
  • bottom feeders

Keeping only one type of fish usually means that a pond requires constant hands-on work and cleaning. We always recommend getting a good mixture of fish and plants for the pond to stay as clear as possible, with a filtration system to remove any excess that the fish cannot clean.

Is Algae Good For A Fish Pond?

Despite the hatred many have for algae; it is an important part of any pond ecosystem that needs to be kept to ensure the fish are healthy. Algae that is naturally in the water will be eaten by many fish, while algae grass is used as a hiding spot for most pond fish, keeping them safe.

This is why you should never filter out all the algae in pond water and why you should not remove all the algae growing on the sides of the pond walls. Instead, finding something that naturally eats the algae will keep the algae in check without causing the entire pond to turn murky.

Further, if you are in an area that is closer to nature, you will find that algae attract other water creatures naturally. Tadpoles are one of the best things to find in your pond, they feed only on plankton and other small plants, creating an ecosystem that becomes self-sufficient.

A close up of a tadpole in a pond with greens.
Finding tadpoles in your pond is a good thing!


The best way to keep your pond clean is to balance fish and plants that keep the algae in constant check. However, cleaning the pond once a month will keep the sediment levels low and the algae that cause green water out of the pond for you and your fish.

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