I have a 135 gallon tank full of Flourite that was set up for a little over 12 years. I think that I had the onset of old tank syndrome, and I decided to clean it.
There was nowhere to put the fish, so I left them in the tank.
I picked up a 6 inch diameter plastic colander from Walmart for about 1 buck.
I started on the left side and worked to the right side.
I was able to get about three scoops out of the tank before there was too much debris floating around.
The filters would clear things up in about 15 to 20 minutes.
I was dumping it into a storage bin, took 4 big bins.
As I came across plants, I just removed them and let them float in the water.
I went slow removing the substrate, as the BB are in substrate, probably more then in the filters.
I also tested for ammonia and nitrite while removing the substrate, but ammonia or nitrite never showed up.
The fish, 5 big Blue Acaras and some other things didn't seem to really care about it, they would swim buy and get in the way.
Finally removed it all, cleaned it buy putting some on a 32 gallon garbage can full of water, hooked up a Vortec diatom filter,
and stirred the substrate until the dirt was out of there.
I actually clogged up the diatom filter, that has never happened before.
Then I put it back in.
Defiantly made a difference, I was able to turn the lights back up and no algae, and the ph went up.
Pulling all of the substrate out cleaning it and putting it back in and replanting everything took about a month.
If you decide to leave the fish in the tank, go slow and test for ammonia and nitrite.