Based on my experience the stuff off the bottom can't be used for anything useful as is until it's been spread out fairly thinly over a large area and allowed to sun bake dry for an extended period. Even then it usually has to be mixed with regular dirt at that point.
Others more knowledgeable will respond as to the hows and whys.
When I cleaned out my sons pond and also my daughters pond, the muck did not want to grow much of anything the first year. But after it weathers a year, it grows stuff really well.
Funny, but I also find that what pure clay that I dig up from a new pond will also not grow hardly anything the first year no matter how hard I try (short of covering with top soil). But after it weathers a year wild grass and especially weeds will start growing.
Maybe the weathering process is important to any dirt that has been deprived of above ground natures processes for a long time.
