rlilia:
I should have said "as opposed to dipping it in a bucket of water that you would have to throw out between plants or just letting the water run through the pot".
As I purchase my RO water from a local store and bring it home in 2 1/2 gallon jugs, I have tried to find the best way to keep from wasting it; I have found that watering enough to get all the medium wet allows a lot of water to run through the pot and goes to waste. So, when I need to really soak a plant I wrap the pot in foil or plastic and then fill the pot with water and let the plant soak for about 20 minutes. Then when I remove the foil I only have to throw out about 1 cup instead of several cups in the "run-through" method. This allows me to conserve as much water as I can, and the long soak also allows the water / solution to penetrate the clay pots I use; the porous clay can hold microbes as bad as any medium.
Now of course I can't take the time to do this every time, but every month or so I "deep water" like this in the summer - in the winter I just spray them well, unless they need treated with fungicide then I use the foil wrap method.
Again, this is just how I do it - I know some will just dunk several plants in the same communal bucket of water, but I lost a huge amount of plants by doing this years ago (over 35 years - God, I am OLD!) and passing mosaic virus to about every plant I had. It only takes one infected plant to contaminate the water - but to each their own.
Basically, to answer JKeys original question - yes, you can soak medium and pots in fungicide without harming the plant, depending on the fungicide you are using. I don't use systemics as I have had no reason to; the old reliable Captan has stopped any fungus I have had and I really don't know about the long term effects of systemics.
Hope this answers your question!
Steve