Does water hold beneficial bacteria?

No - only time it is helpful is when you are cycling since it needs to filter feed into your filters.

Otherwise only other times you have a decent amount of beneficial bacteria in the water is if you just did a gravel vac and you only used a under gravel filter since that is where all of your beneficial bacteria is for this filter type only (otherwise it’s housed in your filter media in your sponge filter/hang on the back/canister).

Negative, it holds it in the start but that’s really about it. Water is just water, and all the vast majority of the beneficial bacteria is held within the filter media you are using (substrate if undergravel filter, of filter pads if using a traditional filter).

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As for the water itself, it's not where the bacteria are found in in fish tank but in the solid surfaces in the aquarium such as decorations, plants, gravel, rocks and filter media.

Quote from NoFishBefore

I keep seeing online people say that you need to keep a certain percentage of the water when moving tanks, or transferring fish, etc. Does water really hold that much beneficial bacteria?

I don't really think water holds too much bacteria because if it does, it might not be safe for the fishes in the water. They will definitely get infected quickly.