If you have severe hardwood floor water damage, repair can be very costly. If there is any deformation which must remove timber and replace it. If only water stains, sandable surface staining, and staining timber again if necessary, and reseal the timber.
It is virtually impossible to cater for yourself if the entire carpet was flooded. If your wall to wall carpet soaked got completely probably be better off just completely removing and replace both the carpet and padding, unless you hire a professional can dry the carpet, padding and sub-soil.
It is actually filling that causes the problems, as it is very difficult to dry, while the majority carpet dry completely well. If possible, you may be able to hire someone who has just arrived and remove and replace the filler, but honestly, it sounds like more and hassle work. You will need to remove the fill, let your existing carpeting completely dry, reinstall the filling.
If the water damage happened on concrete, tile, or laminate, a good disinfectant cleaning after fixing the water source and water sanitation is usually sufficient.