How to Change an Aquarium Filter Without Losing Bacteria

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You’re probably aware of how important bacteria is in a fish tank. It breaks down toxic ammonia into nitrites, and then the nitrites into nitrates which are much less toxic. A lot of this beneficial bacteria in your fish tank will be on the filter, so whenever you change your filter, you want to make sure you retain as much of the bacteria as possible.

The first thing you want to consider is whether or not your filter actually needs replacing. The filter itself won’t need replacing unless it literally doesn’t work, and the media will only need replacing if it is falling apart. And if you need a more powerful filter, you’re better off keeping your current filter and adding a smaller, secondary filter.

If you do need to replace your aquarium filter, the important thing is to keep the media from your old filter in the tank with your new filter for about a month. You can either keep the whole unit in there, or just the media. Another option is to simply use the media from your old filter in the new filter.

Why Is It Important to Prevent Bacteria Loss?

You might already be aware of the importance of beneficial bacteria in a fish tank, but if not, here’s a quick explanation.

Waste from your fish and uneaten food releases ammonia into the water. This ammonia is lethal to your fish. Beneficial bacteria breaks ammonia down into nitrites, and nitrites into nitrates which are less toxic. And then when you perform a water change, many of the nitrates are removed, keeping the water safe for your fish.

Your aquarium filter provides a great environment for bacteria to grow, so when you need to replace the filter, you want to keeps as much bacteria in your tank as possible.

Do You Need to Change the Filter?

There’s a good chance that you don’t actually need to replace your filter or filter media. Many filter manufacturers will recommend changing the media every month or so. Except for chemical filters, this isn’t necessary. The reason manufacturers recommend this is so you spend more money on replacement filter media. As long as the media isn’t falling apart, it won’t need replacing. Instead, give it a thorough rinse once per month in tank water.

Another reason you might think you need a new filter is if your current filter is too small for your tank. In this case, I would actually recommend keeping your current filter and running another small filter along side it. This way you won’t lose the bacteria, but also, if one of the filters stops working, you will have a backup. Another advantage is that you can use one of the old filters that is already colonised with bacteria to get a new tank started more quickly.

Ideally, you don’t want to change your filter, but obviously if your filter has stopped working, you will need to replace it. The rest of this guide will help you with that.

3 Ways to Change a Filter Without Losing Bacteria

There are three ways you can change a filter without losing bacteria. The main thing is to keep the older filter media in your fish tank for a month or so with the new filter.

Option 1

The first option is to leave the old filter in place along side the new filter for a month. This will give time for the new filter to be colonised with bacteria. One thing to watch out for is the flow caused by the filters. If they are creating too much of a flow that it is disturbing your fish, turn down the settings on the filters if you have that option, or you can baffle the filters with filter pads. Unless the old filter is broken or the flow is too strong, it’s a good idea to leave both filters in permanently. If you don’t want to do this, you can remove the old filter after about a month.

Option 2

The second option is to put the media from your old filter into the new filter. The media is where a lot of the bacteria resides. Obviously this will only work if the filter media is the same size and shape for both filters. And of course, this method won’t work if the filter media is falling apart.

Option 3

If your old filter is broken and the media from your old filter doesn’t fit in the new filter, the third option is to place the media from your old filter in the tank next to the new filter. This will allow the new filter to be colonised with bacteria. After a month or so you can remove the old filter media.


Unless your filter is broken or physically falling apart, you probably don’t need to change it. If you need some more filtering power, you’re better off keeping the old filter and running it alongside another small filter. If you really do need to change the filter, to prevent bacteria loss, make sure you keep the old filter media in the tank for about a month.

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