Hedge,
Biological activity in diesel fuel is a well known issue. Even if there is no water in the bottom of the tank, bugs can make some if they get the chance. When they get started they make more and grow more....
It may look like rusty water, but I doubt very much that it is. Adding biocide is a good idea. There is no reason to wait either after treating or before.
If you see evidence of this, then it is a good idea to care spares of all the fuel filters and know exactly what needs to happen if you get fuel bound. Knowing about your fuel system is something every owner should take the time to learn.
Out on ships and boats this is much more important, but it is still a good idea standing on the dirt.
Matt