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I’m looking to remove all my old gravel, ornaments and plants and replacing with new ones, including a new filter.

What’s the best way to do it and best way to store fish whilst doing it? How long will fish be OK out of tank if I put filter and heater into temporary tank?

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The most important will be to keep your beneficial bacteria so you won't have to cycle your tank again.

Fill your temporary tank with water from the main tank and if possible the old filter, so the fishes will still feel at home. Give them some plants or decorations too, so they can still hide. The "temporary" tank should be as comfortable as a real one. They will need a filter and a heater like back in the normal tank. It should even have some substrate, but a light is optional here. Less light will mean less stress for the fish. Be careful and quick when netting out your fishes with the fishnet, this can be very dangerous. Don't feed the fishes in the temporary tank, unless they have been there for 2 weeks or more.

To keep your water alive and cycled, you need to bring the old bacteria in the new habitat. Bacteria are present on the fish and in the water in small quantities, but most importantly they live in: the substrate, the plants and the filter media, which you all plan to replace. You need to keep as much as possible, at least something.

Here are some options to make the transition smooth and allow the good bacteria to repopulate the ecosystem:

  • (least useful, better than nothing) Keep some water from the previous setup, and put it back in the tank after the change. This can be the water of the temporary tank.

  • (most useful, this is where most of the bacteria live) Reuse the cartridges from your old filter in your new filter, or at least some of them. Don't clean them.

  • Reuse the sponge from the filter intake. Don't clean it.

  • Keep some of the gravel. Don't clean it.

  • Keep some of the plants. Don't clean them.

  • Replace first the gravel (the most complicated) and the plants, but continue with your old filter so the bacteria will be kept and reintroduced to the substrate. After a week or three, replace the filter with a new one. The bacteria, having colonized the new substrate, plants and water, will now colonize the new filter.

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    Sorry for you, but the water isn't important here. The real important thing here is the biological filter media, nothing more. He only need to keep this with good water circulation or the bacteria will die. He don't need to keep gravel or plants....
    – Gawey
    Apr 17, 2019 at 6:18
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    @Gawey I just tried to give different options. Water is obviously the least useful, but some water from an established tank is better than nothing at all. I will edit to reflect that.
    – Manuki
    Apr 17, 2019 at 14:38
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To do this safely, you use the water from your tank and the pump from your tank.

It is best if you do not feed your fish from the day before you plan to do this. Do not feed your fish until two days after you have replaced everything you want in your tank.

You might want to lower the temperature by 1-2 °C in your holding tank - this will buy you some extra time to finish the job in the main tank.

You can keep the fish in the holding tank for maximum 48 hours and remember: no food during this time, let your pump run continuously for the duration of the time your fish are in the holding tank. The reason I say 48 hours max is the fish will be stressed when they have to live close to each other in a small space.

Do not clean the pump/filter at all until at least a week after you have finished everything in your main tank; you will need all the good bacteria you have to avoid ammonia and nitrite, and feed very little the two first weeks after this job.

If you are replacing the pump/filter in your main tank you need to use both pump/filters for a week to be sure the biological cycle keeps going in your tank, if it is impossible to run two filters you need to take out the filter media from the old filter and put this into your tank to seed it with bacteria.

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