A study was conducted to examine the removal of methyl tert-butyl ether (MTBE) and 15 other organic compounds, as well as perchlorate ion, in waters of different quality. The 15 organic compounds consisted of halogenated solvents (chlorination), disinfection by-products, pesticides, and nitrosodimethylamine (NDMA). These studies were conducted using a pilot scale 20 kW mobile electron beam system at Water Factory 21, Orange County, CA where wastewater is treated and re-injected into the ground as a barrier to salt water intrusion. Future applications for this treated water include water reuse. Ground water and treated wastewater, after having gone through a reverse osmosis-polishing step (RO permeate), were used to prepare mixtures of the compounds. Using fundamental radiation chemistry, it was possible to examine the factors effecting removal efficiency of all the compounds as well as MTBE destruction and reaction by-product formation and removal. All of the organic compounds were destroyed in the studies and we also observed the destruction of perchlorate ion in one of the waters.