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A number of microbiological issues are of critical importance to crew health and system performance in spacecraft water systems. This presentation will review an array of these concerns which include factors that influence water treatment and disinfection in spaceflight such as biofilm formation and the physiological responses of bacteria in clean water systems. Factors associated with spaceflight like aerosol formation under conditions of microgravity will also be discussed within the context of airborne infections such as Legionellosis. Finally, a spectrum of analytical approaches will be reviewed to provide an evaluation of methodological alternatives that have been suggested or used to detect microorganisms of interest in water systems. These range from classical approaches employing colony formation on specific microbiological growth media to direct (i.e. microscopic) and indirect (e.g. electrochemical) methods as well as the use of molecular approaches and gene probes.