A novel x-ray treatment system utilizes one or more large area flat panel sources of x-ray radiation directed into a target zone. A target substance within the target zone is irradiated with x-ray radiation from the one or more flat panel sources, reducing the biological effects of a contaminant presence therein. The flat panel source comprises an electron source, an electron accelerator, and an electron target medium. The electron source may emit electrons either via field emission or thermionic emission. The x-ray source may operate in transmissive, reflective, or combined transmissive/reflective mode. The use of large area flat panel x-ray sources in the inventive systems allows for decreased installation and operational costs as well as increased efficiency.