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Does Cleaning Your Fish Tank Kill Your Fishes? The Reasons and Solution

Writen By
Carol M. [Fisheries Consultant]

An aquarium is a home for your lovely pets, and thus it requires cleaning when necessary. Fish will enjoy a clean aquarium as it offers several benefits. Again, a sparkling tank free of odor will create an aesthetic environment.

Aquarium cleaning should be done regularly and done in the right manner. Cleaning aims to clear decayed organic wastes, prevent algae growth and accumulation of toxic compounds, etc. However, if you overdo the process, you risk losing your fish.

Let's find out why cleaning can kill your fish and provide a solution. In the end, we will also touch on the best way to clean an aquarium, especially for beginners.

Reasons Why Cleaning a Tank Kills Your Fish and Solutions

There is a process as to how you should clean the aquarium and with a routine. If you fail to follow the procedure, your fish may die as you interfere with the conditions of their habitat. So, some of the reasons that may lead to fish death are wrong cleaning procedures, and they include;

  1. Massive Water Change 

Water changes are important in removing the poisonous waste products accumulated in the tank. Again, adding freshwater helps aerate the tank and helps your fish in respiration. In addition, water changes can be helpful, especially after an infection outbreak, to eliminate the excess medication in the tank.

If you do a massive or routine water change, you may alter the water parameters such as pH, temperature, and water hardness. A sudden change in water quality parameters puts your fish in shock and, finally, death.


  • Perform small water changes frequently of around 5% of the tank volume twice a week. Also, you can do a 10-15% water change once a week. Every month, do a 25-50% water change.
  • Ensure the water you add to the aquarium has the same water parameters as that inside the tank to avoid shocking your fish. Treat your water with a water conditioner to eliminate chlorine and heavy metal before the water changes.
  1. Killing Beneficial Bacterial

These bacteria are necessary for maintaining the nitrogen cycle. The process converts ammonia compounds into less toxic substances. The bacteria mainly live on the substrate, filter, and decorations.

You can kill the bacteria when you use a gravel vacuum to clean the debris on the substrate. Again, if you thoroughly clean the filter simultaneously with the substrate, you will kill a large number of the bacteria.

Without the beneficial bacteria, the nitrogen cycle process will fail and cause the accumulation of ammonia compounds. Since the fish are still eating and excreting, more waste products accumulate, causing a toxic environment that kills your fish.


  • Invest in a quality gravel vacuum for cleaning the tank. Ensure that you siphon a different section of the tank every time you change the water and avoid vacuuming the gravel.
  • After cleaning your tank, you should wait for around two weeks before cleaning your filter. The filter contains beneficial bacteria which will make up for those lost during cleaning.
  • After a few weeks, you should now replace the filter media cleaning the whole unit.


  1. Overcleaning the Tank

Deep cleaning your fish tank can affect the equilibrium of the aquarium. Some people are tempted to dismantle the fish tank and use household cleaners like dish soap to clean the tank. This action will compromise your fish habitat and make it unsafe for living.


Following the routine of water change and cleaning procedure is the best solution. Your tank will always be clean and won't require deep cleaning. Again, be keen on how much feed you give your fish to prevent the accumulation of much waste. Experts recommend feeding the amount your fish can consume in 2-3 minutes as the excess feed will be wasted.

What’s the Correct Cleaning Procedure for Fish Tank?

We have seen improper cleaning of your fish tank can kill your fish. So, if you are a beginner, you may be wondering, “how do I clean my fish tank?". Below are some guidelines on the correct cleaning procedure.

  • Start by disconnecting the heater and filter. There is no need to remove your fish to avoid unnecessary stress; remove 50 % of the water to maintain the beneficial bacteria.
  • If the sides of the tank have algae, you should scrape it off; it's best to use a plastic scraper.
  • Use a gravel vacuum to clean and siphon the dirt and gunk off the gravel.
  • Refill the tank with freshwater with the same water temperatures as that in the tank. Make sure you remove chlorine by using a conditioner or effective de-chlorinator.
  • If the decorations and filter are dirty, you should clean them a few weeks later to avoid killing beneficial bacteria.


We believe this guide has informed you on how to prevent killing your fish as you clean the tank. Fish require a clean environment to survive, but you shouldn't compromise their equilibrium. Avoid killing the beneficial bacteria, massive water changes like emptying the whole tank and deep cleaning. Follow the right cleaning procedure, and your fish will survive.

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HI, I'M Carol M.
Fisheries Consultant
I'm a passionate fisheries consultant with over 5 years of experience in the aquaculture sector. I have been practicing the skills in offering extension services, teaching learners on aquaculture practices and economic empowerment. In my leisure time, I love researching and writing articles on the niche, offering guidance in fish rearing and also watching fish related documentaries.
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