Will the Desert Spring Humidifier affect my furnace filter or rust my duct work?

No. As long as your filter is not severely clogged and dramatically restricting air flow, the evaporated vapor will not condense on the filter. The Desert Spring furnace humidifier is a passive evaporative device. Therefore the air will only carry as much moisture as it can hold in the by-pass air stream, so the moisture will not condense on your duct work. Only active humidification systems such as steam and spray (misting) units can introduce excess moisture when not properly installed or maintained.