Described herein are various methods, systems, and apparatus for reducing and eliminating biofilms from hydrocarbons. A combination of oxidizing agents and radiation of certain wavelengths forms a synergistic reaction. The synergistic reaction generates EMODs, which are effective in reducing microbial count and eliminating or blocking biofilm formation, particularly in anaerobic environments. This synergistic reaction has a relationship to EMOD creation and has a detrimental effect on Microbial Contamination (MC), Microbial Influenced Corrosion (MIC) and biofilm creation. MC, MIC and biofilm can be eliminated or greatly reduced with the treatment methods in or on equipment including pipelines, storage tanks, and refinery processing equipment.