Key Points

• Perform an annual pond cleanout in fall or winter to safely remove fish, drain water, rinse rocks, clear sludge, and clean filters—this restores balance and prevents algae blooms.
• Cooler months reduce fish stress, allowing safe handling while preparing the pond for clear, healthy water in spring.
• Weekly maintenance, such as emptying skimmer baskets, adding beneficial bacteria, and monitoring water quality, keeps your pond healthy between annual cleanouts.

Out with the Muck, In with the Magic

Does your pond look more like a swamp than a backyard oasis as fall rolls in?

Wondering how to clean it without harming your fish or wrecking your ecosystem?

In this post, you’ll get a simple, step-by-step guide to performing a full pond cleanout during the cooler months in the East Bay.

You’ll also learn why this seasonal service is critical for your pond’s health and clarity year-round.

By the end, you’ll feel confident about what to do, when to do it, and how to keep your water clean, clear, and low-maintenance.

Ready to let the pros handle your weekly pond maintenance and fall cleanout?

Call California Aqua Pros or fill out our contact form to book your annual cleanout today.

How to Perform an Annual Pond Cleanout Step-by-Step

Cleaning your pond once a year keeps the entire pond ecosystem in balance, improves pond water quality, and helps your fish thrive.

The best time for a deep clean in the East Bay area is November through February, when fish are less active.

1. Turn Off and Disconnect Electrical Components

Start by turning off the pump, auto-fill valve, IonGen system, and auto-doser if installed.

Disconnect all cords to prevent electrical issues while draining or cleaning.

This protects your equipment and ensures safe handling of the pond during the cleanout.

2. Safely Remove Fish and Place in Holding Tank

Fill a large container or kiddie pool with your current pond water and add an aerator to maintain oxygen levels.

Catch fish with a soft net and transfer them gently.

In sun-soaked spots like Brentwood, keep the fish container shaded under a patio overhang and use mesh or netting to keep raccoons out—especially if you’re near open fields.

3. Drain the Pond

Use a submersible pump to drain the pond.

Make sure the water is directed away from your home, garden beds, or any structures.

Once empty, remove the pump to inspect or clean it separately if needed.

4. Rinse Rocks, Liner, and Features

Use a regular garden hose with a high-pressure nozzle, or a pressure washer, to rinse algae, dirt, and biofilm from rocks, gravel, and pond walls.

Be careful of getting too close to the liner with the pressure washer as you can pierce the lining and create a leak.

Always rinse from top to bottom to push debris downward for removal.

5. Remove Sludge and Debris

Scoop out built-up leaves, sludge, and muck using a pond vacuum or by hand with a small rake or bucket.

Focus on corners, behind rocks, and under aquatic plants where debris tends to settle.

This reduces the organic matter that leads to poor pond water quality and algae blooms.

If you are getting frequent algae blooms, you may be making one of the common pond algae mistakes.

6. Clean the Skimmer and BioFalls Filter

Take out the skimmer net and filter pads for a rinse.

Use a scrub brush or gloved hands to clean inside the skimmer and BioFalls units.

This step is essential to keep your filtration system efficient and your pond clean after refilling.

7. Inspect Equipment for Damage or Wear

Look for signs your backyard pond needs repairs, such as cracks or wear in your liner, check valve seals, pump housing, and pipe fittings.

Replace or repair parts now so you don’t run into failures during the warmer months.

Proper maintenance now prevents bigger problems later.

8. Refill the Pond and Add Treatments

Use dechlorinated water or add a detoxifier if you’re using city tap water.

Once filled, add beneficial bacteria to jumpstart the ecosystem.

Reconnect and restart your pump, IonGen, and auto-doser if applicable.

Ensure everything is flowing properly before continuing.

9. Reintroduce Fish

Float fish in their holding tank or container on the pond surface to let water temperatures equalize.

Slowly release them after 15–20 minutes to avoid shock.

Monitor closely for any signs of stress or illness over the next few days to keep your pond’s health on track.

Why Fall/Winter Is the Best Time for Pond Cleaning in the East Bay Area

Reduced Fish Stress

During cooler weather, fish enter a dormant state, requiring less oxygen and food.

This makes fall and winter the safest time to handle and move them without triggering stress or increasing the risk of fish kill.

Performing a deep clean now protects your pond’s inhabitants.

Prepares Your Pond for Spring

Removing decaying organic material and leaves in the fall prevents nutrient overload in spring, which can fuel algae blooms.

Early cleaning gives you time to fix any issues with filtration or pond equipment before warmer temperatures return.

What’s Included in a Professional Pond Maintenance Service

Weekly Hands-On Cleaning

A weekly service ensures your pond stays balanced between annual cleanouts.

Professionals remove debris, empty skimmer baskets, clean pads, and backwash filters if needed.

This reduces buildup that can affect both water clarity and system performance.

Water Quality Treatments

Specialists add beneficial bacteria weekly to support biological filtration.

Depending on the season and conditions, they may also apply algaecide, muck reducer, phosphate remover, or other products to restore pond water quality without harsh chemicals.

System Inspections and Adjustments

Each visit includes checks on the auto-fill valve, IonGen performance, and auto-doser function.

If anything is blocked or malfunctioning, it can be fixed early before it impacts your fish or aquatic plants.

Optional Add-Ons

You can upgrade to twice-weekly maintenance for higher-debris environments or decorative ponds near trees.

Follow the link to view our pond cleaning checklist to see more details about our weekly pond maintenance service.

Some homeowners also request cobblestone installation to prevent liner erosion or make minor equipment repairs to keep their systems running smoothly.

Easy Weekly Pond Maintenance Tips

Even after a deep clean, light weekly tasks go a long way in keeping your pond clean.

• Empty the skimmer basket once or twice a week to prevent clogs
• Add beneficial bacteria weekly to maintain biological balance
• Monitor clarity and check for green water or floating algae
• Top off water levels and make sure the auto-fill valve is working

These small efforts help reduce stress on your fish and keep the ecosystem healthy between professional services.

Upgrades to Consider During Annual Cleanout Season

Add Shade Plants or Floating Covers

Floating pond plants like water lettuce, water hyacinth, and water lilies help control algae by reducing sunlight exposure.

They also give your fish a place to hide and help maintain cooler temperatures in warmer months.

Install an IonGen G2 System

This device releases a small amount of copper ions to suppress string algae without harming fish or plants when properly set.

It’s ideal for fish ponds with recurring algae issues and integrates well with Aquascape’s ecosystem design.

Add or Upgrade Your Auto-Doser

Auto-dosers reduce the manual effort of pond maintenance by automatically releasing bacteria and clarifiers.

Upgrading yours ensures consistent treatments year-round and helps maintain pond water quality with less guesswork.

Install Fish Caves or Predation Deterrents

Fish caves protect koi and goldfish from predators like raccoons and herons.

For added safety, you can also install motion-activated sprinklers around the pond’s perimeter to scare off curious wildlife without using chemicals or traps.

Pond Maintenance and Cleaning FAQs

How often should I clean out my pond?

Most ponds benefit from one full cleanout per year, ideally between November and February in the East Bay.

If your pond is in a high-debris area, you may need a mid-season refresh.

Note: Clients who enroll in our weekly maintenance program receive a 20% discount on Annual Fall Cleanouts.

Can I shut off my pond in the fall?

No. A pond must run 24/7 to support beneficial bacteria and maintain circulation.

Turning it off can lead to algae growth, stagnant water, and poor water quality.

Will I get mosquitoes in my pond?

Not if your pond stays moving.

Circulation from a properly sized pump prevents mosquito breeding.

You can also add mosquito fish as a natural control method.

How many fish can I have?

A safe rule is one inch of fish per square foot of pond surface.

Overstocking leads to water imbalance, stress, and health issues for your fish.

Schedule Your Fall Cleanout With California Aqua Pros

Staying ahead of seasonal pond maintenance means fewer surprises, clearer water, and healthier fish.

By cleaning your pond in the fall or early winter, you reduce stress on aquatic life, improve overall pond water quality, and set yourself up for success when temperatures rise again.

Whether your pond needs a deep clean or you’re ready to upgrade with smart equipment or plant health boosters, California Aqua Pros offers year-round services that make the job easy.

Whether you live near the San Ramon Valley trail, have a hillside yard in Livermore, or enjoy waterfront views in Discovery Bay, our team of pond experts brings professional care tailored to your pond’s unique environment.