Any medication with antibiotic properties has the potential to adversely affect the biofilter. However, all of our antibiotics should have minimal impact on your beneficial bacteria.
Metronidazole unfortunately is not the best option for treating directly into the water column, as it is really not very water soluble. Instead, I might suggest that you go with PolyGuard. This is a very effective medication for freshwater fish that is easily absorbed through the scales and gills and therefore does not require ingestion. You can read more about PolyGuard here: http://www.seachem.com/Products/prod...PolyGuard.html
Please keep in mind that we cannot guarantee any of our medications to be 100% plant or invertebrate-safe, so if you must treat the entire tank, I would keep an eye on any plants and/or inverts that you have.