Charcoal has been used as an important part of fish filters for decades.
Not all microbes are bad microbes. In fact you want a heathy makeup of microbes.
Now I am assuming you have a system to digest fish waste and/or trap and remove it.
Plants generally only take in what is soluble. So microbes play a key role in going from liquid and solid fish waste to NPK that plant
roots take in.
Roots need oxygen so the warning about low disolved oxygen pockets in your system is valid.
Might want to spot check with a oxygen meter if you have one.
Can also use clean iron rods.
Will rust in water with oxygen. Will turn black in water with no oxygen. It is a old trick to see what soil does over a season.