How to Clean a Pond: The Complete Pond Cleaning Guide

How to Clean a Pond: The Complete Pond Cleaning Guide

Posted on Feb 18th 2020
Author: Bill Hoffman

Life can get busy sometimes and time just gets away from you… Maybe you didn’t have time to cut back your aquatic plants in the fall…Maybe you forgot to put the beneficial water treatment in last summer…Maybe a hole was torn in the net and the pond filled up with leaves. Whatever the reason muck and sludge has built up. There comes a time when you just need to clean it out and start fresh. 

The best time, by far, to do a full pond cleaning is in the spring or fall when pond water temperatures are close to the same as water temps coming from the faucet. This will put less strain on the fish as well as keeping the beneficial bacteria, that is growing in the pond, intact. 


Saving your Fish: 

  • After ensuring that the water quality has been tested and deemed safe, water is drawn from the surface of the pond into stand-alone containers - available to rent at Hoffman’s Water X Scapes if needed. 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.
    • 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.
  • 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.
  • Also, be sure that the containers are not sitting in the full sun.

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.
  • This water can be pumped to the higher levels of the pond, like the waterfall and stream, to wash the muck off of the liner and gravel.
  • When that water is 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.
  • 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.

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 to suck out the bottom of the pond.

  • It will be helpful to move stone around while rinsing to loosen debris and muck.
  • All pond filter media in the waterfall box and skimmer should be cleaned or replaced at this time.
  • 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.

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.
  • 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.

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


Visit us online for all of your pond supplies and pond accessories. We are always happy to answer any water feature or pond questions and are available to help assist in troubleshooting.

We also have temporary fish containers and Pond Vacuums rentals available for your convenience. Don’t want to clean your pond yourself? Let the experts at Hoffman’s Water X Scapes do it for you with our Pond Services