The chapter describes the freshwater and seawater cooling systems where bacteria, fungi, and microalgae are involved in the development of microbial fouling process. Microfouling or microbial fouling pose serious problems in industrial water distribution systems, by reducing the heat transfer efficiency and water flow, thus resulting in substantial drop in the turbine pressure, condenser tube material corrosion, besides effecting the operation of allied systems. Envisaging the nature, of biofilm formation, and its frequency of occurrence will assist in biogeochemical studies, in making innovative cooling water distribution systems, and in setting up of required engineering instrumentation. Microorganisms grow well in the cooling water pipelines, which provide a conducive environment and assist in adhesion as well as colony formation. The growth of microbial inhabitants and their metabolic by-products deteriorate the metallic components of the cooling water structural materials and cause severe failures. The chapter also describes the progression of microbial biofilm development and schematically illustrates the sequence of events in biofilm formation and their implications in industrial water distribution systems. The bacterial consortium residing in the biofilms also plays a role in initiating the corrosion process, since the microorganisms are juxtapositioned at the substratum/biofilm interface. The progression in microbial colonization by biofilm bacteria on the metal surfaces is disparate, and this helps in creating concentration cells with redox potentials that are produced between two different materials. Microbes that stimulate corrosion usually include bacteria, algae, and fungi. The effect of bacterial corrosion in distribution systems results in substantial damage to pipelines and supplementary apparatuses by inducing pitting or underdeposit corrosion. Finally, the chapter elaborates on the monitoring procedures and plausible control methods for microbial fouling process.