Removing Gravel from an Existing Aquarium
Ardan Huck March 14, 2002.

If an aquarium has a fish population and a gravel substrate and you wish to go to a bare bottom (no gravel) setup, the recommended way to remove the gravel is to siphon it out along with water changes. This will prevent dirt and trapped debris in the gravel from entering the water column if you were to "scoop out the gravel." If the dirt and debris were to enter the water column the fish could get sick by ingesting the bacteria-laden material.

Good bacteria also live on the gravel substrate. If you were to remove all the gravel at once it could disrupt the biological cycle (the filter may not have enough good bacteria in it to process ammonia/nitrite). It is best to remove gravel a little at a time.

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