How To Clean A Pond: The Complete Pond Cleaning Guide

A clean, well-maintained pond enhances the beauty of your outdoor space while providing a healthy habitat for fish and aquatic plants. Over time, however, ponds accumulate debris, algae, and sludge, requiring regular cleaning to maintain water quality and ecosystem balance. Whether you’re tackling seasonal maintenance or a full pond overhaul, this complete "How To Clean A Pond" guide will walk you through the steps to restore your pond efficiently and safely. From draining and removing waste to balancing water chemistry, we’ll cover everything you need to know to keep your pond crystal clear and thriving. Let’s dive in!

Tip: Be careful. Everything in your pond is wet so its important to be aware that surfaces can be slippery, especially pond liner.

Keeping  your  Fish Safe: 

• How are your fish doing - behaving normally? Have you tested the water lately? Make sure there is no ammonia and that the pH is between 6 and 8.2. These are two of the most important readings to look at. Ammonia at any level starts to weaken your fish. A high pH with ammonia becomes exponentially toxic to fish. Also, what is the water temperature? The closer the water temperature is to 50 to 55 degrees, the less you have to worry about shocking/stressing your fish during re-acclimation. Fish are like people, too much stress and they are more susceptible to infections and parasites.
•  After ensuring that the water quality is  safe, water is drawn from the surface of the pond into stand-alone containers, such as trash cans, kitty pool or cattle trough. Make sure they are clean, no oils, no soaps and no other toxic substance to fish.. These containers will temporarily house your fish while cleaning your pond. Some of this stored pond water can also be used to wash and refill your pond. This will also help save some of the beneficial bacteria in your pond. If your pond water is clean and of good quality, (no ammonia, no nitrites or nitrates, good pH) the more you can save the better.
• Ammonia and many other toxins are heavier than water, therefor sink to the bottom. This is why the water should be taken from the surface first.
• Pump the water level down to where the fish are confined to a small space. This will prevent having to chase them all over the pond. Less stress on them, less stress on you.
• Once your containers are full, redirect the remaining pond water into the landscape away from the pond. You don’t want this water to run under your empty ponds liner.
• Gently catch your fish with a pond net and place them into the filled containers. If you have a lot of fish, spread them out amongst more than one container.
• If the cleaning will take more than a couple of hours, be sure to move your pond aerator into the tanks.
• Don’t forget to cover the tanks to keep the fish from jumping out onto the ground. And believe me, they will try.
• Also, be sure that the containers are not sitting in the full sun. Water temperature can change drastically and stress the fish.

Saving your Pond Plants:

• After all the fish have been moved, relocate the potted pond plants. 
• Place water lilies and oxygenating pond plants in the deeper water tanks. Marginal pond plants may be set on the ground, or in shallow tubs of water. 
  
  
• This is a great time to divide water lilies and marginals. 

Rinsing the Stone: 

• There should still be some water in the deeper areas of the pond. There should still be 6” to a foot of water.
• This water can be pumped through a hose to (you may need to buy an extra piece of hose – use your pond pump or get an extra pump) blast the sidewalls of your pond and the stream bed.This should loosen the muck and debris and wash it down to the bottom of the pond.
• When that water in the bottom becomes too dirty to do any good, just pump it into the landscape. The waste within the ‘dirty’ water is a fantastic fertilizer.
• If more rinsing is needed, your garden hose may be used, or some of your stored pond water.
• If it has been a few years since your last cleaning, you may need to repeat this process more than once or several times to get most of the muck out.
• We do not recommend “power washing” the inside of your pond - as it is believed to remove most of the beneficial bacteria that takes years to develop in your pond. You may think that getting every last speck of green algae off the rocks is a good idea and prevent it from growing back. Not so. It will come back.

Cleaning the Bottom of your Pond and Filters: 

Once all the stone in the upper levels of the pond have been rinsed to your satisfaction, use a Pond Vacuum with a Gravel Vacuum head (if you have gravel in the bottom of the pond) to suck out the bottom of the pond.

• It will be helpful to move stone around while rinsing to loosen debris and muck. You may need to add more water a couple of times.
• All pond filter media in the waterfall box and skimmer should be cleaned or replaced at this time. Don’t forget to vacuum out these filters, particularly the waterfall box or FilterFalls.
• If you are using lava rock inside of your filter media bags, we recommend replacing it every year to maintain quality of filtration, or switch to using Bio cubes, which are much lighter and reusable.
• If for some reason you are cleaning during mid-season, ONLY use the pond water to rinse the biological pond filter. Temperature differences between the pond water and the water from the garden hose will kill the beneficial bacteria that has already been established. Chlorinated water will also kill the bacteria.

Returning your Fish and Plants to your Pond:

• Use your pump to transfer water from the holding containers back into the pond.
• Once there is enough water in the pond, to at least cover the backs of the fish, they may be re-introduced to the pond. Read “How to Acclimate Koi and Other Fish to Your Pond” for the steps.
• Pump the remaining water from the containers back into the pond.
• Extra water will be needed from your garden hose to finish filling the pond.
• Add water slowly as to not change the water temperatures too quickly. You may need to add water over several hours.
• Add water treatments such as, Pond Basics Water Conditioner or Microbe-Lift's Dechlorinator Plus, as well as a dose of beneficial bacteria like Pond Basics Pond Starter Dry Bacteria.
• Pond plants may be put back in the pond at any time during this step. Sometimes it’s easier to get the water lilies back to their final resting spots before the pond is completely full.
• Get the number of Hornwort up to the recommended rate as soon as possible to slow or prevent algae growth. Cleaning your pond will upset the balance in your pond for a little while, but adding the water treatments and plants will re-establish it’s balance quickly.

Now your pond is clean and you are ready to enjoy the season!