How to Clean a Fish Tank from Waste: Complete Guide 2022

Owning and enjoying an aquarium is an immense pleasure that many enjoy. Watching the fish swim and listening to the murmur of the aerator pump with the light bubbling of the water is refreshing and relaxing. However, there is more to owning an aquarium than just watching the guppies galivanting about in the water; a fish aquarium must be cleaned of fish waste to keep the fish healthy and alive.

So, how to clean a fish tank from waste?

There are two methods to cleaning aquariums, depending on whether you have a freshwater or saltwater fish tank. The first, cleaning a freshwater aquarium, has ten steps, while the instructions for cleansing a saltwater aquarium requires nine.

This article will give detailed instructions on how to clean a fish tank both a freshwater and saltwater aquarium of fish waste, plus methods that allow you to keep the water clean.

10 Steps to Clean Fish Waste From a Freshwater Aquarium

While cleaning a freshwater aquarium seems like a lot of work, it is an inevitable responsibility for anyone who enjoys the pleasure that fish can bring. There are ten steps to the cleaning of a freshwater aquarium, including:

Clean Fish Waste steps

  1. Gathering cleaning supplies
  2. Cleaning the sides of the aquarium from algae and fish waste
  3. Deciding how much water to change
  4. Siphoning out the old water
  5. Cleaning the gravel
  6. Cleaning the decorations
  7. Adding freshwater
  8. Watching the water for cloudiness
  9. Cleaning the exterior
  10. Changing the filters

The steps are outlined and explained in the following sections.

Step 1: Gathering the Cleaning Supplies

To remove the fish waste from an aquarium, the first step is to gather all the cleaning supplies needed to complete the job.

Below is a list of the supplies that are necessary to gather before beginning to clean a freshwater tank. These include all of the following:

  • Water conditioner
  • Treated water
  • An algae scraper (aka an algae pad)
  • A five-gallon bucket
  • A siphon type gravel vacuum
  • Aquarium safe glass cleaner
  • Bleach
  • Metal or plastic razor blade

It is important to remember that all of these items, especially the treated water, must be gathered well ahead of actually changing the water in an aquarium. Now for a look at these items and the specifics of each.

Water Conditioner

The first question one may have is, why do I need to add a water conditioner to my aquarium water? Can’t I just leave it out for a few days and then use it? The answer to these questions is simple, humans add chemicals to our water supply to kill bacteria and viruses, and this cannot be accomplished solely by leaving water sit for a few days.

In fact, the U.S. Fish & Wildlife Service has found that a pint of chlorine would be all that is necessary to poison fish in 20,000 gallons of water. (Source: U.S. Fish & Wildlife Service)

Water conditioner should be added every time a water change or top off is performed in a freshwater aquarium.

Treated Water

As can be seen, adding a water conditioner to treat tap water is essential to the life of the fish in the aquarium. If the water is not treated, it will result in the death of the fish within the aquarium by poisoning from chlorine.

Simply add the water conditioner to the tap water you are going to use before you pour it into the aquarium, making sure to follow the manufacturer’s recommendations on the bottle.

There are four distinct types of water conditioner on the market, including:

  • Dechlorinate
  • Chloramine neutralizer
  • Complete conditioner
  • Reverse osmosis water conditioner

Taking a brief look at all four will help aquarium owners understand better which one to choose.

Dechlorinate. This liquid instantly removes chlorine but does not remove ammonia and heavy metals. If your tap water contains chloramine, a declorinator can cause a dangerous build-up of ammonia.

Chloramine Neutralizer. This substance instantly removes chlorine and breaks down plus neutralizes the ammonia in one of two ways; it binds to the ammonia molecule, and it converts ammonia into ammonium, both substances that are harmless to fish. Some chloramine neutralizers also neutralize heavy metals, but others will not, so it is important to read the package to make sure you are getting what you need.

Complete Conditioner. The most common type of water conditioner used by aquarists is the complete conditioner. This substance does five things:

  • It eliminates chlorine
  • It neutralizes ammonia
  • It detoxifies heavy metals
  • It eliminates copper
  • It protects the fish slime coat
  • It buffers the PH of the water

Some types of complete conditioners neutralize more depending on the product used.

Reverse osmosis water conditioner. While not technically a water conditioner, reverse osmosis water conditioner acts as a re-mineralizer while also removing chlorine, chloramine, and other types of substances poisonous to fish found in tap water. Caution: not all reverse osmosis water conditioners will remove these poisons, so it pays to read the instructions that come with it.

If the reverse osmosis water conditioner does remove chlorine and chloramine, there will be no need to use another water conditioner with it.

Since reverse osmosis removes minerals vital to the health of the fish such as potassium, calcium, sodium, and magnesium, using a reverse osmosis water conditioner is important.

An Algae Scraper (otherwise known as an Algae Pad)

That algae that grow in the aquarium are bad for the fish because algae use dissolved oxygen found in the water to grow, reducing the available oxygen available in the water for the fish. Algae can also produce as a byproduct dangerous toxins that will kill all the fish in the aquarium.

So, it is important to remove the algae from all the pieces of equipment, and the glass inside the fish tank and using an algae scraper is the way to do it.

The algae grow well in aquarium water because there is a constant light source (algae are plants), and the fish waste in the water acts as a potent fertilizer.

A Five-Gallon Bucket

A five-gallon bucket (19 L) is a must-have when changing the water and cleaning the equipment of a fish aquarium. Make certain to use a bucket that is dedicated to cleaning the fish aquarium only.

A Siphon Type Gravel Vacuum

This device will become invaluable when cleaning the fish waste from the gravel at the bottom of the aquarium. Make certain to get a manually operated one and not one that runs on batteries for better quality cleaning.

Aquarium Safe Glass Cleaner

The best aquarium safe glass cleaner is one made from vinegar that can be found in most kitchen cabinets.


While it may seem counterintuitive to use bleach to clean an aquarium, so long as it is washed away completely, it disinfects and cleanses better than most other substances. Plus, bleach breaks down harmless byproducts rapidly.

Metal or Plastic Razor Blade

Since most people who own aquariums utilize algae scrapers and chemicals to loosen fish waste and algae from the insides of the tank, these are considered to be optional pieces of equipment.

Step 2: Cleaning the Insides of the Tank Free of Algae and Fish Waste

After removing 10-20% of the water, using the algae pad, clean along the inside of the aquarium glass, scrubbing as little as necessary to remove any algae that have formed as well as fish waste. If necessary, use a razor blade or plastic blade to scrape any stubborn residue from the glass.

During this process, it may be advantageous to wear plastic gloves dedicated to only the washing of the aquarium to minimize any allergic reactions to the substances that are on the glass or plexiglass sides of the tank. There are shoulder-length versions available for use, specifically in an aquarium.

Step 3: Decide How Much Water You are Going to Change

When deciding how much water needs to be removed from the aquarium, there are three main considerations:

If the aquarium has a large amount of fish, thus a large amount of fish waste, the aquarist should replace 25-50% of the water every week. However, if the goal is to reduce nitrate and phosphate levels, then a larger and more frequent water change is necessary.

Step 4: Siphon Out the Old Water

Using the five-gallon bucket, siphon and direct the water into it. It is vital to remember that the bucket used needs to be dedicated only for use in cleaning the aquarium.

Aquarium siphons should not be battery operated as they offer less control over the speed the water leaves the tank than a mechanical or manually operated siphon.

Later, the same hose and siphon may be used to refill the tank.

Step 5: Clean the Gravel

To remove fish waste, excess food, and other debris, push the gravel vacuum through the gravel. To make certain that no small or delicate fish are sucked into the vacuum, place a clean fishnet over the end of the siphon. Clean about 25-30% of the gravel every month.

If there is sand on the bottom of the tank, lower the flow rate of the water through the siphon by placing a finger over the end of the siphon or kinking and releasing the hose. Hold the hose an inch or less from the sand so as suck up fish waste without disturbing the sand too much.

Running fingers through the gravel will stir it and help release any fish and other waste trapped underneath the gravel.

Step 6: Cleaning the Decorations

Because algae are caused by nutrients from fish waste in the water and light exposure, it will build upon the tank decorations. Avoid using soap to cleanse decorations as it could harm the fish. Instead, wipe the decorations off with the algae pad or a never before used soft-bristled toothbrush in the tank as you remove them.

If the algae are difficult to remove from the decorations, remove them from the aquarium and soak them in a large bucket filled with water and 1/4 cup of bleach for fifteen minutes. Make sure to thoroughly rinse and treat the decorations with chlorine water conditioner. If the decorations are porous in nature, let the items dry completely before returning them to the aquarium.

Step 7: Adding Fresh Water

Replace the water taken out with fresh water that has been treated, and using an aquarium thermometer, make certain before it is placed in the aquarium that it is the same temperature as the water left in the fish tank.

Make certain not to overfill the tank.

Step 8: Watching the Water for Cloudiness

After replacing the water, wait a few hours and watch for any cloudiness that remains to clear. Although there are water clearing agents available, they are unnecessary. However, if the water remains cloudy, it is because there is an underlying problem. In that case, using a clearing agent will only mask the problem and not solve it.

Step 9: Cleaning the Exterior

Cleaning the outside of the aquarium will not be effective in the life of the fish. However, it will make the enjoyment of them better.

Wipe down the outside of the tank, the hood, the light, and the tank top, using a glass cleaner. Be incredibly careful not to get any of the cleaners into the water of the aquarium, and it is recommended to spray glass cleaner onto the rag rather than the aquarium glass itself.

Acrylic tanks may require a special polish to clean them.

Step 10: Changing the Filters

Rinse and replace the mechanical filtration system regularly with tank water to prevent losing favorable bacteria from the water. Remove and replace chemical media such as carbon pellets every two to four weeks, depending upon the number of fish and the waste they will create.

9 Steps to Clean Fish Waste From a Saltwater Aquarium

Saltwater tanks have become popular in recent years and for good reason. The variety of exotic fish is much larger for saltwater, and the colors of corals and the fish themselves are magical. However, owning a saltwater aquarium comes with some special needs, and one of those needs is in the cleaning process.

remove waste with tool

Below we shall discuss the nine steps to cleaning fish waste from a saltwater aquarium including:

  1. Mixing a saltwater solution
  2. Getting the cleaning supplies ready
  3. Cleaning off the algae
  4. Siphoning out the water
  5. Cleaning the gravel
  6. Cleaning the decorations
  7. Checking for salt creep
  8. Adding the water to the tank
  9. Checking the temperatures every day

Some of these steps look quite similar to the instructions for cleaning a freshwater aquarium, and as we shall see, they are, but some steps differ in important ways.

Step 1: Mixing a Saltwater Solution

Before you can begin to clean a saltwater aquarium of fish waste, it is vital to mix a proper saltwater solution. It is important that the salinity, PH, and temperature of the water are made to fall within acceptable limits for the fish.

To start, on the night before the aquarium water change, place the water in a clean plastic bucket dedicated to only being used for the aquarium. Then heat the water with an aquarium heater. Add the salt mix that can be purchased at pet stores being cautious to follow the instructions on the package.

Aerate the water while mixing the salt to help it dissolve better.

The next day, check the salinity with a refractometer, hygrometer, or salinity probe to make sure the salinity is at least 30 grams per liter. If there is going to be corals in the aquarium, then the salt to water concentration needs to be 35 grams per liter.

Check the saltwater solution with a thermometer to make certain the temperature for the fish is between 73-83 F (23-28 C).

Step 2: Getting the Cleaning Supplies Ready

As can be seen, by the following list of cleaning supplies, there are familiar items on the list of things ready for cleaning the fish waste from an aquarium. The items needed are as follows:

  • An algae pad
  • A 5 US gal (19 L) bucket
  • A siphon-type gravel vacuum
  • Filter media
  • A thermometer
  • 10% bleach solution in a separate container
  • Aquarium-safe glass cleaner or a vinegar-based solution
  • pH strips
  • A refractometer, hygrometer, or salinity probe.

It isn’t necessary to explain the first of the components needed to clean fish waste from a saltwater aquarium as they are the same as from a freshwater tank. Instead, we will focus on the last two items on the list, pH strips, and the refractometer.

pH Strips

pH strips are pieces of specialized paper that change color depending on the pH (the acidity or alkalinity) of the water. These litmus test strips are cheap and can be purchased at nearly any department store. They measure rather accurately the pH of any liquid, and using them is vital to the health of the fish in the saltwater aquarium. ( Link)

A Refractometer, Hygrometer, or Salinity Probe

These devices help to measure the density of the water. All three will give different readings if one dissolves different solutions of salt into the water. They do this by measuring the conductivity of electricity through the water, which measures how much water or salt needs to be added.

Step 3: Cleaning off the Fish Waste and Algae

This step is identical to the instructions for a freshwater aquarium. Using an algae pad, gently remove any fish waste and algae from the inside of the tank. One can use a razor blade to remove any stubborn soil but be cautious as the blade might cut the glass and can cause considerable damage to aquariums made from a plastic material such as acrylic.

Step 4: Siphoning Off the Water

Unlike with freshwater aquarium cleaning, only change 10% of the water and do so every two weeks. For most aquariums, this should be enough to eliminate nitrates from the water. To siphon the water, start the siphon manually and allow the water to run into a large bucket.

Step 5: Cleaning the Gravel or Sand

Fish waste, excess food, and other debris must be removed to make the saltwater aquarium clean. Do this by pushing a gravel vacuum through the rocks or sand. To clean sand, hold the hose one inch or less from the surface and suck up the fish waste without disturbing the sand. Stir the sand as you vacuum to prevent the formation of oxygen-poor regions in the water.

Step 6: Cleaning the Decorations

This step is virtually the same as with freshwater aquarium cleaning. Wipe off the decorations with an algae pad or a never before used soft-bristled toothbrush in the tank water that was siphoned out. One can also remove the decorations from the tank and soak them in the 10% bleach solution you have prepared for fifteen minutes. Rinse the decorations well and treat them with a dechlorinating agent.

Step Seven: Check for Salt Creep

Salt creep occurs when water in a saltwater aquarium splashes out of the tank, getting things wet and after the water evaporates leaves behind salt crystals that are highly corrosive and deadly to fish.

Clean the salt off with an algae sponge or a clean wet towel and add back the water that was splashed out.

Step Eight: Adding Water Back to the Tank

Slowly and carefully pour some of the premixed water from step one into the aquarium. Make certain that the mixture has been matched in salinity and temperature to that of the water already in the aquarium.

Avoid overfilling the tank.

Step Nine: Check the Temperature Every Day

It is vital to the health of the fish to check the temperature of the water often, especially in the first twenty-four hours after cleaning the tank and changing the water. Make it a practice to check the temperature of the water in the aquarium daily as saltwater fish live in a very narrow temperature range. Too much or too little heat in the water, and the fish can sicken and die.

The Dangers of Overfeeding Aquarium Fish and the Increase in Fish Waste it Produces

Overfeeding Aquarium Fish

Overfeeding fish is the number one reason aquarium water becomes dirty, and algae grow freely in the tank. Overfeeding is detrimental to the health of the fish and has several negative effects including the following:

Uneaten Fish Food Releases Toxic Ammonia. Ammonia and nitrates are given off as the fish food decomposes, and these substances are dangerous to any aquarium, but especially newer tanks where beneficial bacteria that eat nitrites have not had a chance to develop. This is especially true or smaller aquariums where nitrite or ammonia levels can become lethal quickly.

Decomposing Food Uses Oxygen. Decomposing food lowers the dissolved oxygen content in the water adding stress to the fish. This effect is the most severe in warmer aquariums, such as saltwater tanks, where the water is in the upper 70s to mid-80s.

The Breakdown of Fish Waste Lowers the pH Level. Organic material, such as fish waste, lowers the pH of the water by releasing carbon dioxide that is then converted to carbonic acid. In a saltwater aquarium, the buffering capacity is low, so the pH level can quickly drop below what is safe for the fish.

Uneaten Food Clogs the Filter. A clogged filter decreases its efficiency and reduces the circulation of the water in the aquarium. Decreased circulation of the water may result in lower amounts of dissolved oxygen content, a drop in pH, a rise in ammonia and nitrite levels, and stress for the fish.

Decomposing fish food that is not filtered is an excellent medium for harmful mold and fungus to grow.

Excess Food Contributes to Rising Nitrite and Phosphate Levels. These levels, when high, contribute to an increase in the growth of algae, which results in poor water quality. Poor water quality stunts the growth of fish and causes their colors to fade, plus lowers the fish’s ability to fight disease.

Simple Steps to Lesson Fish Waste in an Aquarium

There are some simple hacks to remember so that an aquarium, either freshwater or saltwater, will keep the fish waste to a minimum, thus avoiding all the problems on the list above.

  • Feed Your Fish Only What They Need. Fish food should only be given to an amount that the fish can consume in two minutes or less, and only once or twice daily.
  • If the fish seem hungry after two minutes, give them a tiny bit more but not enough so that the food rains down to the bottom of the aquarium.
  • Do not feed the fish one or two days a week to allow them to feed on any food that has gone to the bottom of the tank.
  • Always feed according to the number and size of the fish in the aquarium, not how large the tank is in which they live.
  • Choose one responsible person in the home to feed the fish, thus reducing the chances of more than one person overfeeding the fish.
  • Make certain there are plenty of scavengers in the aquarium such as loaches, snails, or shrimp to clean up any food that makes it to the bottom.
  • When switching foods, feed the fish sparingly at first because the fish may not like the new food at first.

Following a few feeding tips and cleaning the aquarium will help keep the fish waste that causes algae and other problems from growing into a major headache and killing the fish in the tank.