How To Clean A Fish Tank

When the aquarium is clean it can look amazing to the eye – both for yourself and for anyone who see’s it.

The trouble is they don’t keep themselves clean do they.

[tag-tec]Fish[/tag-tec], like humans produce waste. This waste along with the aspects which we introduce into the aquarium (uneaten food etc) all helps to increase the pollution in the water.

Of course we introduce an aspect of filtration into the system as well as other nutrient export mechanisms to help keep the water so that it is habitable. You tank however does go through cycles where it can look to be truthful a bit of a mess.

You get various algae blooms – diatom, hair, slime etc all of which come and go and can be kept in line by performing the correct care and maintenance but still there are aspects of the aquarium which need to be kept clean.

The cleaning aspect of the maintenance does depend upon what you have in your aquarium, what filtration method you use etc and I will attempt to cover the basics of cleaning.


Aquarium Glass

The glass will require cleaning. The best way to do this is with a magnetic based glass cleaner. This has a smooth surface on the outside so that the glass/acrylic is not damaged and a rough side on the inside to remove the algae from the glass. The magnets allow the two sides to push together to increase the pressure on the glass to improve the cleaning ability. The good thing about a lot of these types of tools is that if it falls off for whatever reason then the part in the water will float to the top.

The easiest way to use this is regularly. They are good at removing a slight amount of algae but they will not be able to deal with a large amount.

To remove heavier amounts of [tag-ice]algae[/tag-ice] and coralline algae when it is present on the glass is to use some type of blade. The one which I use is a glass scraper which has a long handle with a blade on the end. This allows you to scrape the algae from the glass. When using these types of devices make sure that you do not damage the sealant on the aquarium.

If you use cover glasses then these can be removed from the aquarium and cleaned.

The front glass can be cleaned to remove any water splash which may have occurred. I would not recommend using glass polish from a spray can as some of this may enter the aquarium and could be detrimental to the inhabitants. I personally use a dry cloth to perform an initial clean and then another clean cloth to polish the glass.


Cleaning of the [tag-self]substrate[/tag-self] depends upon the type of substrate you have implemented. If you have installed a deep sand bed then you should never clean this yourself. You should try and breed enough life in the sand to clean it for you.

If you do not have a deep sand bed installed then it will over time become full of detritus, uneaten food etc. This will need to be removed from the aquarium so that it does not break down and cause spikes in your water parameters.

The best time to do this is when you are doing a water change. With a piece of wood or some other suitable device you can slowly stir the sand – not to much to create a sand storm but just enough to bring the ‘bad stuff’ out of the sand. Once it is in the water column do your best to siphon as mush away as possible.

You will not, of course be able to catch it all but do your best perhaps working on a section of the sand at a time during each water change.


If you are using live rock as your filtration and have purchase some ‘clean up crew’ then these should do a very good job of keeping the rocks clean as long as you have put enough in in relation to the size of your aquarium.

If you spot and detritus, sand etc on the rocks then you can either siphon this off during a water change, blow it off with a power head or waft it away using your hand. Once in the water column it can be siphoned away.


This does depend upon your filtration method. If you are using live rock or a deep sand bed then natural based cleaning should be used. If, however you are using filtration such as a canister filter etc then these will need to be manually cleaned.

To do this simply turn off the filtration unit and, dependant upon the design of the filtration unit remove the filtration chambers. Inside the chambers will be the filtration media. It is absolutly imperative that the filtration media is not washed in tap water. It must be cleaned in old aquarium water. The reason for this is that the ‘life’ on the filtration media will be destroyed when washed in tap water.

Clean it in old aquarium water until it is clean, then clean both the insude and outside of the filtration chambers and filtration itself – you can use tap water for this part.

If the filtration device has an intake then this may be protected via a sponge prefilter of some type. You do not want this to become active and become a filter itself so these need to be washed in tap water until they are clean.


This is quite often an overlooked part. Your aquarium may (or may not be) placed on a very nice aquarium stand. This may become dusty. Don’t reach for the wood polish and spray the wood. Wipe it off instead with a damp cloth. The reason for this is that some of the polish may find it’s way into the aquarium water and be detrimental.

I have heard on a few occasions of aquarists having problems with air fresheners. Not the spray type but the ones you place on the shelf, window ledge etc. They work and do make you home smell nice but they get into the water and can be detrimental.

A while ago I was speaking with a friend of mine in the fish shop and no matter what he tried he could not get his corals to come out. Myself and the shop owner helped him as much as we could – testing the water, checking the setup – everything we could thing of and they still would not come out. In the end we found out by accident that it was the air freshener. It was not anything we did but it had run out and within days the corals came out.

If you think about it then it makes sense. At the water surface is where the air exchange takes place. If there is other elements in the air they they will go into the water as well. Goes to show how delicate aquatic life can be.

Anyway to close cleaning the aquarium can at times become a bit of a chore. It does not need to be. It does not take long as long as you keep on top of it and let’s face it our aquariums look a lot nicer when they are clean don’t they?

  1. We’ve cleaned our freshwater aquarium twice and each time the fish soonafter died.
    Apparently we left something deadly behind.
    Can you please suggest which cleaner / technique is best as we are novices and hate learning the hard (and expensive!) way.

    Thank you
    Mike and Donna

  2. Sorry to hear that you have been losing fish.

    When you say you have been cleaning the aquarium is this physically cleaning the equipment, gravel etc or are you doing maintenance i.e. water changes.

    What filter medium are you using in the aquarium?

    If it is something like an internal/external filter then are you cleaning the filter in old aquarium water or under the tap. If it is the latter then this will kill all the filtration bacteria which could be a cause.

    Is you filter medium under gravel filtration. if so then are you cleaning the gravel in the aquarium. This could be effecting the filtration.

    When doing water changes do you add the relevant additives to the water prior to changing the water. These additives remove all the harmful aspects in the water.

    What I would recommend and this does depend upon your system setup is :

    1. Change 10% of the water weekly ensuring that you use a suitable additive to make it safe for fish.

    2. Clean the filter medium in the water you have just taken out of the aquarium when you did the water change.

    3. Physically clean the glass using a correct tool like an aquarium magnet or scraper.

    4. Clean the gravel in the aquarium using an aquarium gravel cleaner to remove all waste.

    5. Test your water parameters.

    If you can give me some more information as to what you do and how your system is set up then I will be able to give you better advice but I hope this helps.


  3. Hi Peter, my name is Alex. I just got my new 65 gal saltwater fishtank with 83 pounds of live rock in there, it’s been cycling for 3 weeks. Anyway i added 3 snails and 3 hermit crabs for starters, live sand (about 3 inches deep) turned brown on top, i went to my local fishstore they told me i need a sandsifting starfish and a cucamber! ( weird thing never seen it before!) so i got those two and I bought additional 4 snails and a clownfish………and now i wonder is my tank going to spike with ammonia, are my creatures in it going to be ok? Is the brown stuff going to go away? I mean, the fishstore told me it was ok….but i don’t know, so i thought i might ask you.
    Thank you!



  5. Hi.

    Cleaning up an ex marine aquarium shouldn’t be too hard but could need patience and a bit of time.

    Fill the aquarium to the brim with fresh water (tap water will do) and this should dissolve a lot of the residues over time.

    The residue left will need rubbing with a rough cloth to assist it to let go. Any areas that are particularly stubborn soak in vinegar as best you can. You may need to resort in some areas to a knife or similar, but if doing this be careful not to scratch the glass/acrylic and avoid damaging any silicone seals.

    Once all clear a good rinse in fresh water is required.

  6. Hi Alex.

    The stuff on the sand you describe as brown is possibly a golden brown. This is likely to be diatoms, and will go away fairly quickly once the silicate has been used up.

    The bio load you have is not large. If you have prepared your bio-filtration properly you should not have a problem. Just continue to monitor ammonia, nitrite and nitrate, plus pH. The only good reading for the first two is nil, as these are the dangerous toxic ones. Nitrate should ideally be kept at 10ppm or less, as it is a nutrient for nuisance algae. pH should be stable in the area of 8.1 to 8.4.

    Routine seawater changes should also be completed weekly, changing about 10% of the net aquarium gallonage.

    Please feed carefully – overfeeding causes pollution and problems.

  7. Thank you John!


  8. Guys i have a question, i have 2 percula clowns one is larger and more darker in color, the other one is smaller and lighter in color. Anyway i supposes they are a pair cuz they sleep together and don’t fight ….but just a day ago the larger clown just started sitting by the anemone and the smaller one is just sitting at the top in the corner with his nose down, closely paying attention to the larger clown….is this a breeding behaviour? because they didn’t eat much in the last day

    thank you!

  9. Hi Alex,

    It does sound like it – I hope so anyway.

    Quite often clownfish when they pair up do become different sizes with the larger one being the female. The female can become protective and at time aggressive when ‘brooding’ and the male does often tend to stay away but keep a look out.

    What I would recommend is to monitor them closely and see if you can locate any eggs anywhere. Quite often the female will choose a location which she finds suitable and then thoroughly clean it prior to laying the eggs. At this point the fish will become very defensive as they protect their eggs and will even have a go at the reefers hand when it is placed to close.

    Have a think as well in relation to what you will do if they are breeding. Will you leave them in the aquarium and hope for the best or attempt to remove them and place them into a breeder where you can care for them.

    Keep an eye on them and let us know how it progresses.

    Excellent news if little clownfish are on the horizon.

  10. well only when i turn off the lights for the night the 2 clowns come together and sleep in the anemone. but i don’t know it is going to be bad if i leave the little fish in the big tank? and what do you mean “hope for the best”? something might hurt them in a big tank?


  11. Hi Alex,

    If the clown fish do breed then initially there will be loads of eggs stuck to the rocks in the aquarium, When they hatch there will be loads of little fish in the aquarium.

    There may be other fish in the aquarium which may eat them. They may get sucked into an overflow, protein skimmer etc.

    If they are removed from the aquarium and placed into a breeder tank then there will be nothing to hurt them and they will be able to grow and get stronger.

  12. Evening,

    I have heavy algea on the insde of my 20 gallon tank with two 11 year old regular goldfish in it. The first question is, historically I’ve been using a white cloth rag to clean the algea, but these days the fish do not seem to react, to it very well, so can I use a clean razor blade instead of a glass scraper to clean the algea, and don’t I need to remove the algea from the tank as it is seperatged from the glass? The second question is, can I buy a safe algea eating fish like those that suck on the walls and rocks or perhaps a snail, or will their presence and waste disrupt my goldfish environment.

    Thanks in advance for insight offered!

  13. Hi,

    A lot of this depends upon what the aquarium is made from. If it is glass then yes a razor blade can be used, if it is acrylic then the blade may scratch the acrylic.

    Another one to consider is the use of an algae magnet. The cleaning aspect in on the inside of the aquarium and the handle is on the outside – therefore you do not need to put your hands in the aquarium which the fish will appreicate.

    With regards to your second question then yes there are animals which can be used to assist with the cleaning of the aquarium glass/acrylic however you need to consider if the aquarium will happily take another fish without stressing the filtration. Also consider that once the algae is gone that the fish will need to be fed algae food to keep it heallthy.

    Hope this helps,


  14. Hi All…….Ive just inherited an empty 50L Marine tank..(interpet 50)…it has a lot of dry fungi looking deposits on the inside of the glass. How do i completely clean the tank before using it ? It is a year or two old and has been ‘without fish’ for a couple of weeks or so. I am a complete novice…although have sucessfully kept coldwater fish in the past….thanks in anticipation….D.

  15. Hello Darren.

    This sounds like calcarous deposits.I suggest you fill the aquarium with cold fresh water to a level above the deposits and leave it for a few days. Then use an aquarium razor scraper (beware of silicone seals!) which should remove it. If any is particularly stubborn use some vinegar, this should defeat it.

    Then if you wish to ensure the aquarium is sterile, empty all the fresh water out and leave it empty and dry for two weeks. Nasties that are relevant to salt water cannot stand dessication. Actually, the soaking in fresh water should do them down anyway.

  16. ive just put sand in my aquarium tank and im just wondering what is the best way to get debris and poop off the bottom of it…. also what depth should the sad be …. thanx dean

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