How to Clean a Freshwater Fish Tank (A Step by Step Guide)

How to clean a freshwater fish tank without removing your fish

Do you want to know how to clean a freshwater fish tank without removing your fish?  You may not know this, but keeping your fish in their home is not lazy fish keeping.  This method is better for both you and your fish.  These six easy steps on how to clean your fish tank will give you less work and keep your fish happy too; and happy fish means a happy, healthy aquarium.

Many fish tank beginners will start off with a secondhand fish tank, and for experienced hobbyists who have older fish tanks, you may run into a few problems too.  This guide teaches you not only how to clean a secondhand or older fish tank, but we include general freshwater aquarium maintenanceThis will include how to repair a leaking aquarium with a quick fix and a permanent solution; and how to disinfect an aquarium useful if you have a disease or pest outbreak.

A Step by Step guide on How to clean a freshwater fish tank without removing your fish

You need to clean your fish tank but don’t want to remove your fish?  You can do this by cleaning your freshwater fish tank in a similar way to how you would clean a saltwater aquarium.  However, there are a few differences which is why I have created a separate article for people who have freshwater aquariums.

How to clean a freshwater fish tank

All the products you will need to clean your freshwater fish tank are listed before we dive into the 6 easy steps that teach you the best way to remove algae and other debris from your aquarium.

Products you will need to clean a freshwater fish tank:

  • Siphon or tank vacuum
  • A gravel rake or glass/acrylic scraper
  • A toothbrush or similar brush
  • Either of the following vinegar, bleach or an aquarium cleaner
  • Magnetic float
  • A clean bucket of water and either a vinegar or bleach solution
  • A bucket filled  with one of the following: dechlorinated, filtered, or RODI water at room temperature (for more information about the different types of water you can use in a fish tank read How to Clean a Saltwater Fish Tank (A Step by Step Guide)

The Six effortless steps to a perfectly clean aquarium

Step #1: Remove all the elements in and attached to your fish tank

Remove all the various attachments you have on your fish tank as you will have to remove algae from them.  The first thing you do is lift off the lid from the tank.  Turn off, then remove your pump.  Open the filter bracket and remove the filter.  The order of the steps may differ depending on the setup of your aquarium. 

Clean the lid and pump with a brush and clean water.  If you have stubborn patches, use bleach, vinegar, or an aquarium cleaner (if you use any of these products rinse well with clean running water.)  Clean or change the filter as appropriate for your fish tank.

Leave all of these bits and bobs in a safe area to dry, this will allow the chlorine to breakdown into less harmful chemicals.

Step #2:  Clean the decorations in the fish tank

Artificial decorations can be covered with algae and other slime and need to be cleaned.  Remove all the different plastic plants, rocks and other non-living decorations from your fish tank, and place them into the bucket filled with a water solution to soak while you remove algae from the glass. 

To clean algae off rocks, use a bit of aquarium water and a brush to scrub off the algae and slime and place them back into the water.

Step #3:  Clean the glass of your fish tank

If you want to enjoy watching your fish swim around, you need to clean algae from your fish tank glass. This will keep the environment in your aquarium clean. 

Use the scraper and magnetic glass cleaner to clean the glass around your tank.  If you have an acrylic fish tank, use acrylic equipment to scrape the algae from your glass.  Wait for all the sediment to settle before siphoning or vacuuming fish tank sand.

Step #4: cleaning aquarium decorations with vinegar

Your decorations have been given time to soak, and you are ready to scrub the algae from them.  Use a toothbrush or similar small brush to scrub your decorations.  Rinse well with clean running water and set them aside to dry.

Step #5:  Siphon 25% to 30% of the water

Vacuuming your sand will remove algae and waste from your sand.  This will not only clean but keep the environment and levels within the fish tank stable.  This is where cleaning a freshwater and a saltwater tank differs. 

If you have a saltwater tank, you only drain about 10% of the water weekly, but with a freshwater aquarium, you can drain more water less often.  This will depend on the amount of waste the inhabitants create and how much waste you remove when cleaning.  Watch the nitrate levels, and when they are high this will signal you have to clean your fish tank.

Thoroughly siphon the sand to remove as much waste and debris as possible, vacuum the sand until you remove 25% of the water into a bucket.  Discard the wastewater and fill up the tank with clean water.

Step #6:  tidy up the sand and restore your fish tank

Flatten and neaten the sand in your aquarium.  Replace all your decorations in a new order to create variety for your fish.  Once you are happy close the lid and replace the pump and filter.  Turn on your pump, and you have a clean fish tank.

Also read – Best 20 Gallon Fish Tanks for Beginners

Your tank will be cloudy in the beginning, but within a few hours, it will clear.  However, if you don’t want to wait that long, use a few drops of Freshwater Aquarium Water Clarifier, and your tank will be crystal clear.


  • Replace your carbon filter every month.
  • If you use bleach, vinegar or a chemical aquarium cleaner, rinse all the products and allow them to dry before returning it to the tank to prevent contamination.

Most of the time, you will keep your fish tank clean using the steps above, and your fish can swim around happily without you troubling them.  Once in a while, you may have to drain your tank and give it a good clean. 

It’s a good idea to keep a tank ready to fill with the water from your display tank if you need to clean your tank or in an emergency; for example, your tank has sprung a leak.  Add in a few decorations for the fish to hide in, and it will do for temporary accommodation.

How to Make your own aquarium filter:

Cleaning your filter is not fun and it is cheap enough to replace if you make your own.  This is an effective and cleanest way of cleaning a fish tank filter.

The products you will need to create your own carbon filter are:

  • Slip the filter bag over the cartridge
  • Fill the bag with fresh carbon
  • clip the filter into place and you are done. 

How To Clean a secondhand aquarium

Many reefing journeys begin with a secondhand aquarium.  Whether you find it at a yard sale, or if one of your relatives gifted you a secondhand one to get you started.  Either way, you will have to clean your fish tank to get it looking new.

Check for leaks this forms part of your freshwater fish tank careBoth salt and freshwater tanks are prone to leaking, and before you do anything carry the tank outside.  If you do this inside and it leaks, you could end up with a mess.  Fill the tank all the way to the top with water. 

Fast leaks will show up quickly but leave it standing outside for a week or two to find the slow ones.  Once you have determined there are no leaks, check the silicone seals around your tank. 

Have a look at the silicone around the tank.  If there is any lifting or bubbling, it may be a good idea to reseal the aquarium before filling it up with water and fish.  At the best of times, silicon will only last 10 years.  This time may vary depending on the weather (difference in temperature between hot and cold) and the length of time the fish tank was stored.  Replacing it before you add any fish to it may save you trouble later.

Signs the silicone of your fish tank needs to be replaced:

  • You can run your fingernail under it in a few places
  • The silicone is no longer clear but white or foggy in some areas
  • The silicone is lifting
  • You have a slow or fast leak

If any of these are true, you have to reseal your tank (don’t worry, it is not as hard as you think).  You may want to reseal it anyway to keep the silicone neat and tidy.  If you don’t need to fix the silicone and you have no leaks, go right ahead to cleaning and maybe disinfecting your aquarium. 

The products you will need to clean an empty fish tank

  • A clean sponge (you want to know what products you are putting into your tank)
  • A toothbrush or similar product
  • Vinegar, bleach or an aquarium cleaner
  • A clean bucket of water to which you add either vinegar, bleach or an aquarium cleaner
  • A hose connected to a faucet
  • A spray bottle filled with clean water

How to clean a secondhand aquarium

If you have been given decorations for your fish tank too, allow them to soak before you clean all the different decorations in your fish tank with hot water and a brush.

Alternate between spraying the tank with the bottle filled with clean water and using the sponge to scrub all the glass, including the bottom, corners, and sides of the tank.  This will remove most of the muck. 

Once you have finished cleaning your fish tank, spray with a hosepipe to clean the loose debris from the tank.  Look at your fish tank and see if there are any areas that need more attention.  Scrub these areas again. 

On persistent stains, try using vinegar or bleach and salt as an abrasive and continue.  Salt is safe to use to clean your freshwater fish tank as it rinses off easily.  Scrape a blade to remove hard water stains off aquarium glass.

Once you have removed all the muck rinse well with the hose.   Dry and polish the glass using vinegar for a streak-free finish.  Using these steps to clean your fish tank with a little time and some elbow grease, it should be as good as new.

This tank has a life and history you do not know.  You could expose your fish to harmful illness and bacteria which can lead to costly bills and even destroy your aquarium before you have had a chance to get started. 

After you clean your fish tank, it is a good idea to disinfect it and remove all bacteria and other materials that could make your fish sick.

How to disinfect an aquarium

If you have had an outbreak of disease or anything else, you may not only want to clean your aquarium, but you may want to disinfect it too.

The products you will need are:

  • A siphon
  • A spray bottle
  • Bleach
  • Cloth and or sponge

How to disinfect your secondhand aquarium

You need to disinfect all the products that may be contaminated including, filters, heaters and decorations, as well as the products you used to clean your tank.  WARNING Bleach may cause discoloration.  Do not bleach porous materials like driftwood and live plants.

Make a bleach solution in your fish tank and leave to soak.  Empty the tank and rinse it a few times with clean running water and allow to dry. 

Soak all the separate pieces in a bucket with a bleach solution, then rinse well and allow to dry and sit before putting them back into your aquarium.  The time you allow it to sit gives the bleach and chlorine time to evaporate before it can contaminate your fish.

You have no other choice but to remove and replace all material filters with new ones.  The same applies to a substrate that cannot be disinfected effectively replace it too.

Run bleach water through your system to disinfect your tanks.  After that, run the system with clean water using a dechlorinate  for a few hours example, the  Seachem Prime Fresh and Saltwater Conditioner.  It will take about two weeks for the system to dry completely.  Chlorine and other trace metals may actually kill your fish, so it is better to wait before reattaching it.

How to repair or reseal a leaking fish tank

If you have a glass tank and it develops a leak, all is not lost. You can repair it.  

A quick patch fix for an existing fish tank

Freshwater aquarium tip if you need to patch a leak and the leak is higher than the 10% mark of your fish tank, you can do a patch fix without taking your fish out.  This should only be done in an emergency, and it is not recommended. 

Drain the fish tank to the 20% mark.  Silicone the area where you are experiencing the leak and allow it to dry overnight.  Top up your tank with water.  This will only buy you time before conducting a full repair.  New silicone does not adhere to old silicone well, and this patch will not hold for long.

How to reseal a fish tank

Prevention is always better than a cure, and the same can be said for leaking aquariums.   Store your fish tank on a level surface that is strong enough to hold it (with water it’s heavy).  If a level surface is not possible, keep the four corners of your aquarium touching the surface it stands on.  Movement will damage the frame and, over time, cause the silicone to separate and thus create a leak.

Moving your fish to a temporary tank

If you are repairing an old fish tank, you may have to move your fish to another one before you can reseal or repair your display tank.  This requires creating a new space for your fish that can house them for at least three days.

Fill a large enough container with water and allow it to cycle as with preparing a new tank.  Move your decorations to the temporary home.  Catch and add your fish to it, starting with the passive fish moving to the more aggressive ones as you go.  You don’t want them to feel like they are in competition for food so feed them.


  • Check that the more aggressive fish are not attacking the less aggressive ones, or house them separately
  • In an emergency fill a container with the water from your fish tank to move fish across quickly

Products you need to reseal a secondhand or old Freshwater tank

How to reseal a secondhand or old Freshwater tank

A reseal is basically to replace your visible silicone with new silicone.

Step # 1:  how to remove the old silicone from a freshwater aquarium

Cut through the silicone on each side of all the seals of your fish tank cutting the silicone off.  It is important not to push the blade into the seam of the tank, this is what keeps your tank together.  Run a clean blade over the edges to remove the excess silicone.  After you have scraped off as much as you can, wipe the edges with the cloth damp with acetone to clean it.  Wait for the acetone to evaporate.

Step # 2: Create a guide using tape

Decide how thick you want to create your seal (usually around the same thickness as your glass).  Tape an edge on both sides of each join of your aquarium glass leaving this gap in the corner. 

Step # 3:  Apply new silicone to create a new seal

Apply silicone along the base of your fish tank first, then up each of the sides.  Use a silicone edger (or finger) along the silicone to create a smooth and neat finish.  Carefully remove the tape.  You need to work quickly as silicone will form a skin within 10 minutes.

Silicone drying times vary, most people suggest that it takes 24 hours.  Here I would error on the side of caution and wait 48 hours to allow the silicone to cure completely before adding water to it.  You don’t want to see your hard work undone.

How to rebuild an aquarium

If resealing the fish tank is not enough to repair the leak, you may have to rebuild it.  During freshwater maintenance other reasons may cause the need to rebuild your fish tank, and these include replacing a cracked panel or if you want to salvage parts to build a new aquarium.

Also read – How to Build Your Own DIY Fish Tank – A Step by Step Guide

Taking your fish tank apart in four easy steps

This is the first step to rebuilding an aquarium. The products you will need to take apart your fish tank are: Taping knives like the Matrix Drywall Taping Knife and the Mini Razor Scraper.

Step #1:  Remove the trim from your fish tank

To remove the trim from the top of your fish tank, slide the taping knife along both the inside and outside of the trim to cut it free of the silicone.  Be careful with the top part of the trim if you are planning to save it do not cut it.  Edge each of the sides carefully, and the top of the trim will lift from the tank.

Step # 2:  Remove the silicone from the edges

Cut through the silicone on each side of all the seals of your fish tank cutting the silicone off.  At this point, do not clean your fish tank glass of excess silicone, we will do that in a later step.

Step # 3:  Remove the bottom trim from your fish tank

Flip your tank upside down and cut the silicone-free as you did with the top trim and ease it off.

Step # 4:  Remove the bottom pane of glass

Using a razor blade cut through the silicone between the bottom pane of glass from the rest of it.  Lift it off the rest of the fish tank and store it in a safe place.

Step # 5:  Pulling the rest of the glass apart

Gently push against the corners of the tank alternating between the sides to create larger gaps between them.  Once these gaps are large enough, simply cut through the silicone to separate the panes.  Store each one safely.

Step # 6: Clean the glass

This is a good opportunity to remove algae and hard water stains off aquarium glass in all the impossible to reach areas.

Scrape all the silicone, hard water stains and algae from the glass with a blade.  If you need to use vinegar, bleach, or an aquarium cleaner to help you get the glass shipshape, rinse well and allow the glass to dry before you use acetone to make sure all the silicone is off.  Wipe the glass with vinegar for a streak clean finish.  Remember, vinegar changes the PH levels of a freshwater tank.

How to rebuild your fish tank

Now that you have taken your fish tank apart, you can rebuild it and repair any leaks or broken panes.

Things you will need to rebuild a freshwater aquarium
  • Silicone
  • Silicone gun
  • Painters Tape
  • Right angle
Steps to rebuild a freshwater aquarium:

Now that you have the clean glass, you can assemble the tank.  An extra pair of hands will help you with this process, but you could do it on your own.

Step #1:  Preparing the glass and tools

Clean the fish tank glass with acetone and allow it to evaporate.  Line up your tools and glass within easy reach of your work surface.

Step #2:  Prepare the bottom pane of glass

Place the bottom pane of glass on a flat working surface.  Tape a neat edge around the bottom layer to create a guide.  Lay additional strips of tape sticking out from under the glass, the sticky part facing up along all sides.  This will tape the glass in place as the silicone dries.

Step # 3:  Silicone the first corner edge

Shoot an L line of silicone on the bottom pane of glass and a line down the side edge of the back pane of glass.  Put the back pane of glass on the silicone edge of the bottom pane, tape the side glass by lifting the additional strips of tape up against the glass. 

Place the side pane of glass on top of the silicon on the bottom one and the back pane and tape the glass in place.  Hold the right angle against the glass and push the panes together until they are square.  Add more tape to hold the structure in place.  Remove the excess silicone.

Step #4:  Silicone the second corner edge

Run a bead of silicone along the edge of the bottom and the back pane of glass.  Add the side glass and use the tape to hold the glass in place.  Square the corner and add more tape and remove the excess silicone.

Step #5:  Silicone the third and fourth corner edge

This will complete the structure.  Run a bead of silicon on the bottom and each side of the front edge of the glass and add the front pane of glass on top of this bead.  Square off each corner add extra tape and remove the excess silicone.

Step #6:  Seal the fish tank

The fish tank has been put back together, and all we have to do now is seal it.  Follow the steps as laid out in the section How to reseal a secondhand or old Freshwater tank.

Wait for 48 hours for the silicone to cure before filling the aquarium with water outside to check for leaks.


  • Use more silicone rather than less to prevent leaks
  • This is not recommended for tanks smaller than 30 gallons

Freshen up your glass with a wipe down, and you have a new looking aquarium.

Things to consider when you begin this hobby

No matter which aquarium you have or the reason you are beginning this hobby, there are important things you need to think about before you begin.

Also read – 10 Best All in One Aquariums

Things to consider when you are buying a fish tank

Most people will start with a small concept and grow larger, but this leads to extra expenses and may develop problems for you and your fish later.  If you have a small fish tank, but you have high waste creating fish, you will have a hard time cleaning your fish tank.  Consider your end goal and what type of aquarium you want to set up. 

Contrary to popular belief starting with a smaller fish tank is only easier if you are keeping a small number of fish with a low waste output, or you will be cleaning your tank more often.  Goldfish do not belong in small tanks.  If you are planning to keep more fish, start with a 55-gallon tank.

Think about where you are planning to keep your fish tank.  A 55-gallon fish tank is heavy without water.  The surface you plan to use to keep your aquarium on must be able to carry the weight of the tank with water and give you enough space to move around it. 

Direct sunlight will help algae grow, and you should avoid any area by a window or glass door if you do not want to spend all your time cleaning your fish tank.  Add a few cleaner fish and creatures to help you support the habitat.

Also read – Self Cleaning Fish Tanks That Actually Work

You will require a tank where you can keep new arrivals, keep them in quarantine for 6 to 8 weeks before introducing them into your display tank.  This should allow any infections or parasites to appear without infecting the rest of your fish and contaminate your tank. 

You can use the same tank to keep and treat sick fish.  Keep this tank as empty as possible and use a PVC pipe to give the fish a place to hide.  Clean and disinfect the tank and all the equipment you used with it once your fish have been removed.  Keep this additional tank and equipment in a safe, clean area if you need it later.

Things to consider when you are buying fish

Don’t buy fish without researching them.  You need to give them the correct amount of space, food and habitat. If you do not provide enough space, the fish’s organs will grow, but the body will be stunted, and this will cause them to die. 

More aggressive fish can kill passive fish if there is a competition for food and space.  Careful planning of your habitat is important.  Fish, even in the same species have different needs.  This includes the size of their habitat; this encompasses the length and depth of the water.  The type of food they need and what hiding or living spaces they will want.

Don’t forget to purchase the correct type of fish food for each of the different types of fish you have.

Things to consider when building your habitat

After you have decided on your end goal and what types of fish you want to include in your fish tank, you can turn your attention to the decorations you want to add.

The best fish tank decorations

Whether you decide to use real or plastic decorations or a combination of both, each has its own pros and cons.

Think about live plants, in addition to helping you keep your fish tank clean, plants provide hiding places, and a bit to nibble on between feeding.  This will require a real substrate like the Eco Complete Planted Black and not artificial gravel.  In addition to a liquid fertilizer like Aqueon Aquarium Plant Food. Some tools to plant and for occasional pruning similar to Aquascape Tools but no additional cleaning as with plastic plants.

If you are selecting artificial plants and gravel, consider the color in contrast to the color of your fish.  You want your fish to be the stars of the fish tank, and selecting decorations that blend into the background or contrast the fish will allow them to stand out.

Either way, decorations not only make your tank look pretty, but they also provide places for your fish to hide making them less stressed.  As in humans, stress causes fish to become sick and require treatment.

Frequently Asked Questions:

Can I use vinegar to clean my aquarium? You can use vinegar to clean your aquarium if you have no fish in it (or bleach) as long as you rinse it off well to prevent it from entering your fish tank.

If you have fish, vinegar will create more acid in your fish tank.  You can clean decorations and other elements you remove from your tank with vinegar as long as you rinse well. 

Using vinegar to clean your glass is pointless, you cannot contaminate your tank with than 1ml per gallon of water is not recommended, and a drop of vinegar in a liter bottle is not going to help you clean it.  You have two options, keep your fish tank clean or remove all your fish and complete a deep clean of your fish tank.

Can fish hear you? Yes, fish can hear you.  People often think that just because you cannot see the fish’s ears, they cannot hear you.  Fish have internal ears and can hear you through their bodies.

Concluding thoughts on cleaning a freshwater aquarium

Remember when cleaning your freshwater aquarium that both bleach and vinegar maybe harmful to your fish.  Rinse with clean running water well and completely dry naturally before thinking about using it. 

You may be asking yourself why dry fish tank and decorations before putting them back into the water.  The decorations being dry is not the important part, but this gives chlorine time to breakdown into less harmful components.  Tap water is cleaned using chlorine.  If you use RODI as you rinse water, you can skip this step.

There are many wonderful sea creatures and fish you can add to your fish tank.  Each with their own personalities.  Watching fish and other aquarium critters develop and interact with each other is a fascinating hobby.  With a little planning and know how the work involved is easy.

Also read – Glass vs. Acrylic Aquariums – Which One is a Better Choice?

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