How to Deep Clean Aquarium Hardware: Step-by-Step Guide

Today, I am going to perform a deep cleaning on one of my aquariums.

I have let the maintenance lapse a little more than usual.

My process will involve cleaning the glass inlets and outlets, the filter, and other hardware.

The focus is not on regular maintenance but on the thorough cleaning of all the equipment associated with the aquarium.

Welcome to the less glamorous side of aquascaping.

I will take apart all the components.

I plan to remove the carbon dioxide diffuser, the skimmer, the filter inlets and outlets, and the filter unit itself.

My goal is to clean every piece thoroughly before reinstalling it.

What is the Time Limit for Cleaning an Aquarium Filter?

The window between stopping your filtration and restarting it should be no more than 2 hours.

This timeframe allows the beneficial bacteria in your filter to survive without a fresh flow of water.

In a smaller aquarium, it is possible to clean everything at once.

However, for a home setup, my recommendation is to clean all other components first, and then, after you are finished, proceed with cleaning the filter.

Following this sequence makes more sense from a timing perspective.

How Do You Prepare an Aquarium for Deep Cleaning?

First, I unplug the carbon dioxide system and the skimmer to ensure they do not run while being removed.

For the filtration system, it is very important to unplug the filter before closing the hose adapter.

If you do it in the reverse order, the impeller continues to rotate without water, which can cause it to overheat.

A few seconds of this is not an issue, but forgetting and leaving it in that state for hours can seriously damage your filter.

With the filter unplugged, I can now rotate the lock on the hose adapter.

After removing the adapter, I can pull the filter unit away. It is quite heavy because it is full of water and filter media.

I need to collect some water from the aquarium in a bucket.

The reason for doing so is that the filter media can be safely cleaned in aquarium water.

You should never clean your filter media under tap water, as the chlorine will instantly kill all the beneficial bacteria and ruin your aquarium’s ecosystem.

What are the Best Tools for Cleaning an Aquarium?

I have a few specific tools that I use for cleaning the tank.

What is an Algae Scraper Used For?

The first tool is an algae scraper, which consists of a handle and replaceable blades.

You insert a blade into the handle and can then scrape any excess algae from the glass, moving from top to bottom.

Another option for the same purpose is a magnetic algae scraper.

Its design involves two pieces.

One piece is placed against the glass inside the tank, while the other is placed on the same spot from the outside.

By moving the outer piece, you can control the inner piece to clean the glass.

What Brushes Should You Use for an Aquarium?

I also use different types of brushes.

One of them is a simple soft brush, which is good for cleaning the corners of the aquarium.

You should never use a bladed algae scraper in the corners, as you can damage the silicone sealant of the tank.

A soft brush is perfect for this task.

I also use a couple of sturdier brushes.

One is soft but much more rigid than the simple brush, while the other is a metal brush.

These are excellent for cleaning wood pieces.

For instance, if I see snail eggs on the wood, a sturdy brush removes them in a second.

When Should You Use a Cleaning Sponge?

A final tool in my kit is a cleaning sponge.

It is effective for removing dust algae from the sides of the tank; a single wipe is often all it takes.

How Do You Clean Aquarium Glassware and Accessories?

I perform all of my cleaning in the bathroom.

I recommend not doing this work in the middle of your living room.

I have a container full of a cleaning solution, which is Green Aqua Cleanit dissolved in water.

How Do You Clean a Carbon Dioxide Diffuser?

I use the cleaning solution specifically for the carbon dioxide diffusers.

I begin by removing both suction cups, as the solution can damage them.

Using a chemical cleaner is the only way to properly clean your diffuser.

Imagine if you were to rub it by hand or with a sponge; you would clog the fine pores of the ceramic disc on top.

For this reason, you must submerge it in a solution designed for such items.

The cleaning agent works by diffusing through the small pores on the diffuser’s surface, cleaning it from the inside out.

I simply place the diffuser in the solution and let it soak.

The standard recommended dilution is one capful of the cleaning product to 500 milliliters of water, which will clean the item in about 30 to 60 minutes.

You could also use a weaker solution and leave the item to soak overnight.

In my current situation, I am using a much more concentrated solution.

As a result, I only need to leave the diffuser in for about 10 to 15 minutes for it to become completely clean. I will let it soak while I clean everything else.

How Do You Clean Filter Inlets and Outlets?

The filter inlet has become quite ugly.

First, I remove what I can by hand.

To get rid of the remaining internal residue, you will need a flexible spring brush.

Many commercially available hose cleaners are designed for plastic filter hoses and have a very strong spring.

If you were to use one of those on a glass pipe, it would likely break.

The brush I am using is very soft and flimsy, which allows it to bend easily inside the glassware.

To use it, you just insert it and begin pushing it in while also turning it, occasionally pulling it back slightly.

It is important not to force it.

Whenever you feel resistance, use slow and careful movements to work through the blockage.

Sometimes, what appears to be dirt on the inside of the glass is actually on the outside.

For external cleaning, I like to use a regular kitchen sponge.

It is perfect for rubbing the exterior.

One word of caution: some sponges come pre-loaded with a cleaning agent.

Do not use such products.

Those types of cleaning agents are harmful to an aquarium, so only use plain sponges that do not contain any additives.

How Do You Clean an Aquarium Skimmer?

Cleaning a skimmer should be a more frequent task than cleaning the filter or its inlets and outlets.

Removing accumulated plant matter takes only a moment under water.

The effort is minimal, but the results are miraculous for the skimmer’s performance.

It truly should be cleaned regularly.

At my gallery, we clean all skimmers daily to prevent them from clogging with plant debris.

The heart of the skimmer is a small piece of sponge that collects most of the dirt.

Submerge it, squeeze it a few times, and it is clean.

Reinsert the sponge, replace the top, and the skimmer cleaning is complete.

How Do You Clean a Thermometer and Drop Checker?

My thermometer also needs cleaning.

It sometimes gets a bit dirty on the outside, but it is not difficult to simply wipe it clean.

Next, I have my drop checker, which is much more tricky.

You have to empty the reagent from it completely.

With some effort, you might be able to get a small piece of sponge inside.

One of my drop checkers is a nano size, which is particularly difficult to clean.

You can also use a small brush, but do not force it.

Guide it in as far as it will comfortably go.

The interior should not have any algae or dirt, because one part of the chamber holds the reagent and the other holds air.

Algae can only grow where there is water, so cleaning the lower portion is usually sufficient.

There is often more dirt on the exterior, and again, a sponge is helpful for cleaning it off.

The most important step for the drop checker is ensuring it is completely dry on the inside before you refill it.

Your best option is to leave it out for a full day to dry properly before adding new reagent.

How Do You Clean Filter Hoses?

The last items to clean are the filter hoses.

For this job, I use a specific hose brush.

It is quite different from the flexible spring brush I mentioned for glassware.

A proper hose brush is much stronger.

If you were to try cleaning glassware with it, you would definitely break it.

For durable filter hoses, however, it is perfect.

What is the Final Step for Cleaned Glassware?

By now, the diffuser is clean.

Whenever you clean glassware with a chemical solution, you must rinse it under water very thoroughly.

The best practice is to also treat it with a water conditioner that removes chlorine, such as Seachem Prime.

Once treated, the glassware is definitely safe to use again.

How Do You Deep Clean an Aquarium Filter?

I now take the filter and pour out all the water from inside it.

How Do You Clean a Pre-Filter?

First, I unlock and remove the pre-filter.

You can do this by pushing in on the two sides, which allows the bottom to come off.

The contents are not very nice.

I remove all the sponges.

My process is to simply take the sponges and squeeze them in the bucket of aquarium water.

A large amount of debris comes out, and the difference is immediately visible.

The sponges do not need to be any cleaner.

With one finished, I go through the rest.

Sometimes, a sponge can no longer be cleaned effectively and needs to be replaced.

I would say this is necessary when they become permanently deformed.

If a sponge does not return to its original shape after being squeezed, it is time to replace it with a new one.

I reassemble the pre-filter now; it is important to remember how many sponges there were, because it is difficult to see inside the murky water of the bucket.

That completes the pre-filter cleaning.

How Do You Clean the Main Filter Media?

After cleaning the pre-filter, I start disassembling the main filter body by taking off the head.

Whether the plastic components are perfectly clean does not affect performance, but it is much nicer when they are.

With my OASE BioMaster filter, the only regular cleaning required is the pre-filter I just finished.

That is a task you would do about once every month or two, depending on your aquarium.

A full deep cleaning of the main media is not something you have to do often.

I move to the first media basket, which contains an orange sponge.

I just squeeze it in the aquarium water.

It is now clean, so I immediately reinstall the sponge in its basket.

In other types of filters, a component like an orange sponge might instead be a fine filter mesh.

The important difference is that a fine filter mesh cannot be cleaned; it must be replaced every single time.

How Do You Clean Biological Filter Media?

Now I move on to the Seachem Purigen and Seachem Matrix media.

This part gets really ugly. You just need to rinse the media bags.

The Purigen needs to be regenerated periodically.

When you can no longer see the original white color of the beads, it is time for regeneration.

The brownish coating on the Matrix is the actual beneficial bacteria colony that keeps your water clean.

For that reason, the Matrix itself should never be scrubbed clean.

What you do is take the media bag and simply rinse it in the bucket of aquarium water.

The goal is to wash away any loose debris that may have gotten stuck between the pieces of Matrix, not to sterilize it.

How Do You Keep Filter Baskets in Order?

Even though I poured most of the water out of the filter canister, some was trapped because I had not yet removed the media baskets.

I am going to pour out the remaining water.

With my BioMaster filter, all the baskets are identical, so the order of reassembly is not important.

However, in some filters the order is crucial.

For those situations, what I always recommend is laying the baskets out in the order you remove them.

You can place the top one first, then the second from the top next to it, and so on.

Following this small trick ensures that you can put them back in the correct sequence.

Otherwise, you might get them mixed up, and your filter may not seal properly when you try to close it.

This method simply makes the process easier.

How Do You Clean the Filter Impeller?

There is one final task: cleaning the impeller.

You can access it by flipping over the head of the filter; it is always located on the bottom.

You release the cover, clean it, and then remove the impeller itself along with its shaft.

My BioMaster has a metallic shaft, so it does not break easily.

Other filter models use ceramic shafts, so you must be very gentle when pulling them out.

Also, pay attention to the rubber grommets on the ends of the shaft, as they sometimes get stuck inside the filter head or the cover.

It is crucial that you do not lose them.

If you misplace a grommet, the impeller will rotate unevenly during operation, which creates a lot of noise and is not good for the filter.

Put everything back in its proper place. That completes the filter cleaning process.

Reinstalling Your Clean Equipment

The entire cleaning process took about one hour.

Now I will start reinstalling everything on the aquarium.

The tank is refilled, all components are plugged back in, and everything is clean.

This is the method I use to truly deep clean an aquarium.

You can add this knowledge to what you know about regular maintenance.

By combining the two approaches, you can deep clean your tank and make it feel brand new once again.

Conclusion

For a complete deep-clean of your aquarium hardware, shut off and disassemble all components—CO₂ diffuser, skimmer, filter inlets/outlets, hoses, and filter unit.

Soak delicate parts like ceramic diffusers in an aquarium-safe cleaning solution for 10–60 minutes before rinsing and conditioning them with a dechlorinator.

Use soft, flexible brushes to remove algae from glassware and corners, spring brushes for internal pipe residue (never forcing them), and sturdy hose brushes only on durable tubing.

Clean all filter media and beneficial bacteria by squeezing sponges and rinsing media bags in bucket-harvested tank water (never tap water) to protect your biofilm.

Reassemble and restart filtration within two hours to preserve bacterial colonies.