Described herein are various methods, systems, and apparatus for reducing and eliminating, microbes, minerals, chemicals and biofilms from contaminated substances. A combination of oxidizing agents and radiation of certain wavelengths forming a synergistic reaction. The synergistic reaction generates EMODs, which are effective in reducing microbial count, unwanted mineral or chemical concentrations and eliminating or blocking biofilm formation, particularly in anaerobic environments. The synergistic reaction produces long lasting EMODs thereby creating a residual effect. This synergistic reaction has a relationship to EMOD creation and has a detrimental effect on microbial contamination (MC), mineral contamination (MINC), chemical contamination (CC), microbial influenced corrosion (MIC) and biofilm creation. MC, MINC, CC, MIC and biofilm can be eliminated or greatly reduced with the treatment methods in or on equipment including pipelines, storage tanks, supplying systems, cooling systems, and processing equipment.