Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
Couple of ways to do this.
There is a lot of nitrifying bacteria living on the upper layer of the gravel. Even if you decide to remove all the gravel I would keep some, skimmed from the upper layer, in a mesh bag or nylon stocking in the tank for several weeks to help transition the bacteria.
To make the transition gradual, may take a week or longer.
1) Put a piece of pipe, like 1-1/2" to 2" PVC in the tank, bury one end in the gravel and leave the other end out of the water. Sort of shove the gravel aside so there is not much inside the pipe.
2) Pour in well rinsed new substrate through the pipe. Not very much at any one location.
3) Move the pipe into several places until you have done as much as is reasonable at one time. Perhaps the water is starting to cloud a bit.
4) Give the filter several hours or a day to clear the water and repeat.
Remove everything from the tank and redo it all.
New substrate, rocks, driftwood...
Just a little water, not even enough to show above the substrate
Plant, misting as needed.
Put a plate or plastic bag over the substrate and fill slowly. Water seeps over the edges of the plate and there is very little clouding.
Add equipment, then fish.
Hang the retained gravel in an area of good water flow. Or, use it as a cap, if you like that sort of look.