The Complete Guide to Cleaning an Aquaponics Fish Tank

A fish tank is one of the essential components of any aquaponics unit. Apart from accommodating the fish, a fish tank is also a nutrient reservoir, as the fish waste and nutrient-rich water collect here before it’s pumped to the growing beds. Therefore, it’s recommendable to always keep the fish tank clean and in good shape.

Here are 6 essential ways of cleaning your aquaponics fish tank:

  1. Remove uneaten fish food.
  2. Get rid of algae.
  3. Maintain water quality.
  4. Change the water.
  5. Clean the filter, pipes, and pump.
  6. Maintain a sustainable stocking density.

Proper maintenance of your aquaponics fish tank will contribute to a healthy and viable food production system. This article is a complete guide on how to keep your fish tank sparkling clean. Let’s dive in!

1. Remove Uneaten Fish Food

Aquaponics is a combined form of agriculture where you rear fish and grow plants. Feeding your fish appropriately is vital in providing nutrients to the plants in your aquaponics system

However, determining the ideal feed portion can be an uphill task, especially when you want to save on costs by minimizing food wastage.

Despite identifying the dietary requirements of your fish, buying the best quality fish food, or following a strict feeding schedule, there’ll always be some leftovers in the fish tank. The food may float or sink in the fish tank based on whether it consists of fish flakes or pellets.

Letting the uneaten food stay in the food tank for a long period is not advisable because of the following negative effects:

  • The leftovers eventually ferment or decay, degrading the water quality in the fish tank. The decomposition products may include carbon dioxide, which forms carbonic acid when it dissolves in water. The acid alters the pH of the fish tank water, making it unfavorable for fish survival.
  • The breakdown of this uneaten food consumes oxygen, leading to decreased amounts of dissolved oxygen in the water. You will notice some fish moving closer to the surface and gasping for air.
  • The leftovers may clog the filters, leading to a build-up of waste in the fish tank.
  • The accumulation of fish feed means that there’ll be a lot of nutrients, including nitrates and phosphorus. It will cause other organisms like algae and snails to invade your fish tank.

Since uneaten food significantly contributes to poor water quality, removing them after every feeding time is one of the best ways to keep an aquaponics fish tank clean. You can do this at least twice per day, as that’s the recommendable fish feeding schedule. Allow your fish to eat as much as possible within the first ten minutes and then remove the leftovers after 30 minutes.

You can avoid having a lot of leftover fish feed by refraining from over-feeding your fish. The amount of fish food will depend on several factors, including the fish species, dietary needs, age, environmental conditions, and the type or number of plants in your aquaponic system. This won’t only cut the cost of buying fish feeds but will also keep your fish and fish tank in good condition.

It’s also advisable to monitor the feeding habits of your fish to determine the best time to remove the uneaten food. Fish will feed readily when the temperatures are a bit higher (during summer) and when they’re actively growing. So, if you notice a change in their appetite, it could mean that the water quality is poor or the fish are unwell.

To remove uneaten food from your fish tank, follow the steps below:

  1. Scoop the floating food leftovers (fish flakes) using a fine mesh fish net.
  2. Suck the uneaten food at the bottom of the fish tank using a siphon or gravel vacuum – it’s a simple and quick method of cleaning a fish tank.

Check out this YouTube video demonstrating how to use a siphon to remove a deposit of fish feed leftovers from the tank:

Note: The siphoning method is also effective when removing other solid residues, including decaying plant debris at the bottom of the tank.

2. Get Rid of Algae

Algae are one of the sneaky species that invade most fish tanks. Although their presence is normal, they’re fast-growing, making them such a nuisance when uncontrolled. The organisms are mostly prevalent in fish tanks exposed to sunlight (a lot of light) and have nutrient-rich water.

Different algae species exist and invade fish tanks, including green algae, hair algae, black beard, and brown diatom algae. Almost all these algal types occur due to a nutrient imbalance or unfavorable water conditions. However, some may still manifest when the water conditions are perfect, making it difficult to get rid of them completely.

Algal bloom in any aquaponics tank is a problem as it offsets the natural balance of the natural ecosystem that this form of agriculture establishes.

Therefore, it poses a challenge because the algae:

  • Cause pH fluctuations in the fish tank water, creating an unfavorable environment for the fish species in the tank
  • Deprive the plants of the nutrients meant for them in the system since algae feed on the same nutrients as plants, including nitrates and phosphorus
  • Cover various parts of the tank and clog the pipes, hoses, and pumps, impeding water flow and the provision of nutrients to the grow beds
  • Reduce the concentration of dissolved oxygen (DO) in the fish tank, as they use it for respiration. Low DO amounts are detrimental to plants and fish.

Since algae are a menace in fish tanks, removing them should be a part of your daily fish tank-cleaning routine. Otherwise, they’ll colonize the whole system if unmanaged, leading to an unhealthy aquaponics unit. Consequently, fish and plants may die due to oxygen deprivation, nutrient deprivations, and unfavorable living conditions.

Algae Removal Methods

Here are ways to remove algae from your fish tank:

Hand Removal

You could simply remove algae from the fish tank by hand if it hasn’t spread extensively. The only downside is that this isn’t a long-term solution, as it’s time-consuming and labor-intensive.

Mechanical filtration

Mechanical filters are effective components in aquaponic fish tanks. They consist of screens, filters, and settlement tanks that help prevent the invasion or spread of algae in fish tanks. Apart from mature algae, these tools also remove spores from the water.

Covering the Fish Tank

Algae thrive in fish tanks with maximum exposure to light (especially sunlight). You can hinder their growth by placing an opaque material over the tank. You can also move your fish tank (if portable) to a darker location to avoid algae infestation.

Using Humic Acid

Humic acid is a dark brown and water-soluble substance. Apart from being a great addition to soils to increase plant yield, humic acid effectively removes algae from fish tanks. The acid darkens the water, preventing algae from accessing sunlight.

With a UV Filter Tube

A UV filter tube an ultraviolet lamp that emits UV rays, sterilizing the water in a fish tank. The filter tube gets rid of algal spores invading the tank and halts the reproduction and spread of algae in your aquaponics system.

Introducing Algae Eaters

You can also introduce some algae-eating organisms to prevent their growth. These include shrimps and some fish species. However, it’s a short-term solution, as these organisms have different nutrient needs when they mature.

Best Ways to Avoid Algea

Due to their fast growth rates, controlling algae invasion in your aquaponic fish tank can be a painstaking process, so prevention is always the best remedy.

To prevent algae from sneaking into your fish tank:

Avoid Over-Feeding Your Fish

Feeding your fish just the right amount will minimize any surplus nutrients in your tank, hindering algae infestation.

Shade Your Fish Tank

When establishing a new aquaponics system, ensure that the fish tank isn’t exposed to direct sunlight or too much light. You can use an opaque material or dull-colored plastic to cover your fish tank.

Install an Effective Mechanical Filter

Although mechanical filtration is also effective in removing algae from fish tanks, it’s better at preventing their invasion. When installing your aquaponic unit, ensure that a viable mechanical filter is in place.

3. Maintain Water Quality

Water is the ‘life-blood’ of every aquaponic system since it’s the medium through which fish and plants obtain nutrients. Poor water quality contributes to the downfall and eventual collapse of an aquaponic unit. Therefore, maintaining good water quality doesn’t only keep your fish tank clean but healthy too.

Water quality refers to the levels of parameters in water, including temperature, pH, dissolved oxygen, hardness, and nitrogen concentrations.

Water quality is appropriate when these parameters are at the optimum levels, depending on the environmental requirements of the specific fish and plant species in the tank. Conversely, the water quality deteriorates when these parameters fluctuate, making it unfavorable for the organisms to survive or thrive.

Since different fish and plant species have particular environmental needs, it’s recommended to understand water chemistry. You need to know how to balance the parameters contributing to water quality to create a conducive environment for your fish. Testing and monitoring water quality must also be a daily or weekly routine.

The FAO (Food and Agriculture Organization) recommends checking the water temperature weekly to determine whether it’s appropriate for the fish to live. The organization also advises aquaponic farmers to test other parameters, including pH, ammonia, nitrate, and nitrite levels, weekly (especially before feeding the fish).

Here are some things to consider when evaluating water quality:

Fish Waste, Uneaten Food, and Plant Debris

The accumulation of fish waste, uneaten food, and plant debris alters the pH levels of the water in your fish tank. The pH will rise above neutral (more than 7.0), resulting from increased ammonia levels. Therefore, it’s advisable to clean the filter tanks and remove the accumulated organic matter to revert the pH to its optimum level.

Deposit of Organic Solids

The deposit of organic solids in your fish tank reduces the amount of DO in the water, also degrading the water quality. The solids, including fish feces, food leftovers, and other organic matter, use oxygen during their decomposition processes. They’ll also consume the oxygen that nitrifying bacteria use to convert the wastes (ammonia) into useful nutrients (nitrates), which plants feed on.

Reduced DO levels

You’ll know that the DO levels in your fish tank have reduced drastically when you notice the fish spending more time near the surface or gasping for air. The water might also have a foul smell due to the accumulation of decomposing organic matter. It’s crucial to eliminate these wastes using the methods discussed above, once or twice per week.

Another way to increase the DO levels in your fish tank is by improving its aeration. You can use a submersible tank to pump the water and facilitate air circulation. Alternatively, add some air stones in the water to provide oxygen.

Note: A freshwater test kit is your go-to testing kit when monitoring the water quality of your fish tank. You can get all-inclusive test kits that comprise several reagents to test different parameters such as ammonia, nitrite, nitrate, and pH levels.

4. Change the Water

Aquaponics is a system that mimics a natural ecosystem where waste-rich water is filtered, purified, and recycled. You don’t even have to change the water in your fish tank, as it’s a self-cleaning system. However, some circumstances may require you to change the water in your aquaponics unit.

Here are reasons why or situations in which you may need to change the water in your aquaponics system:

During Severe Algae Invasion

Algae invasion can reach uncontrollable levels where all removal measures yield no fruits. In such a case, you may need to change the water on your system to salvage your fish and plants. But, you shouldn’t remove the fish from the tank, as it would stress them out.

Since aquaponics is a water-efficient food production system, you can repurpose the water you remove from your fish tank. You can use it to irrigate soil-based trees, vegetables, or flowering plants on your farm.

When Restarting Your System

If you’ve shut down your aquaponics unit (maybe during winter) and want to set up and start afresh, you can change the water in the system. Also, your system could have collapsed due to poor cycling or an imbalance. This situation could lead to the death of fish and plants; you can choose to re-establish your unit in such a case.

When There Is a Build-Up of Salts in the System

If your fish tank has a high fish volume, fecal wastes, salts, and other organic matter may accumulate quickly. Also, if your plant volume doesn’t match the wastes produced, these will build up and settle at the bottom of the tank.

If this situation continues for a long time, the water quality in your fish tank will deteriorate drastically, requiring some water change.

Here’s how to change the water in your aquaponics system:

Grab Your Tools & Materials

First, you’ll need to gather the required tools or materials. These include a siphon/gravel vacuum, a thermometer, a small tank or a dedicated 5-gallon (18.9 L) bucket, and a testing kit.

Prepare the New and Clean Water

You must first test the water to ensure that all the parameters are within the optimum range. The best type of water to use is rainwater.

However, if only tap water is available, let it sit for at least 24 hours for the chlorine to dissipate, or use a water conditioner or carbon filter if it contains other minerals. In addition to the parameters, test the water temperature using a thermometer to determine whether it’s appropriate for the specific fish breed(s) in your tank.

Remove Waste

Using a siphon/gravel vacuum, remove fecal and other organic matter that has settled at the bottom of the fish tank. And, while siphoning, remove about 15-25% of the tank’s total volume. However, be gentle and don’t remove excess water, as it would disrupt the bacterial colony (biofilter) in your aquaponics system.

Replace Removed Water With New Water

You should test the water again to ensure that all the parameters are optimum. Water change should occur when necessary or once per week for regular maintenance.

5. Clean the Filter, Pipes, and Pump

Filters, pipes, and pumps are common and effective components in most aquaponic designs. Mechanical filters come in handy when sieving out solid wastes when the water leaves the fish tank to the grow beds. On the other hand, pipes and pumps facilitate the smooth flow of water.

Although aquaponics is a self-cleaning system, the build-up of solid wastes on some occasions may be too much for the filters to handle. Additionally, the invasion and spread of algae may reach uncontrollable levels. Therefore, at some point, the filters, pipes, and pumps may become clogged up by solid wastes or algae.

Clogged-up plumbing components impede the water dynamics in an aquaponics system. The water pump will be under pressure to drive water from the tank to the grow beds. The substances clogging the pipes will also prevent minerals from reaching the plants.

So, it’s advisable to clean these plumbing components to unclog them. Cleaning removes the solids or bio slime and facilitates a good water flow. You can use some tools to clean these parts, including a barrel cleaner or a cleaning brush.

6. Maintain a Sustainable Stocking Density

Some aquaponics systems, such as Deep Water Culture (DWC), work best with a high fish stocking density. However, a large volume of fish may lead to overcrowding if the fish tank is small.

This causes several problems, including:

  • Over-production of ammonia: High ammonia concentrations stress the fish, leading to poor health and fish death.
  • Increased fecal waste: This waste degrades the water quality by reducing the amount of dissolved oxygen.
  • An imbalanced aquaponics system: When the fish are more than the plants, there’ll be a nutrient surplus, attracting invading species into the fish tank.

Minimizing the number of fish is an effective way to maintain optimum ammonia levels in your fish tank. It also helps to keep the water clean and improve its quality. So if you notice overcrowding in your fish tank, remove some fish and either sell or consume them.


Cleaning your fish tank should be a fundamental part of your daily, weekly, or monthly routine.

Although an aquaponics system is self-cleaning, you can take additional measures to keep your fish tank clean by:

  • Removing food leftovers
  • Getting rid of algae
  • Maintaining water quality
  • Changing the water
  • Cleaning the filter, pipes, and pump
  • Maintaining a sustainable stocking density

Alexander Picot

Alexander Picot is the founder of and its lead content writer. He created the website in 2022 as a resource for horticulture lovers and beginners alike, compiling all the gardening tips he discovered over the years. Alex has a passion for caring for plants, turning backyards into feel-good places, and sharing his knowledge with the rest of the world.

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