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Microbial quality in the distribution system is a reflection of raw source water characteristics, treatment process configurations, and the physical conditions within the distribution system. Using case studies, the author discusses various biofilm problems that relate to chlorine demand; seasonal fluctuations in raw water pH; cold water temperatures (which decreases disinfection effects); treatment modifications to optimize reductions in disinfection byproduct formation; changes in the point of application of disinfection; the use of granular activated carbon filters (which may provide opportunities for specialized microbial populations to become predominant) or biological activated carbon; and disinfectant alternatives (chlorine dioxide, potassium permanganate, and ozone). Adverse effects on water quality in the distribution system may accrue from reduction in treatment barrier redundancies or attempts to control the formation of disinfection byproducts. Adverse water quality in the distribution system may eventually lead to biofilm colonization of pipe sections, taste and odor complaints and increased coliform occurrences. Additional case studies are used to illustrate this problem.