Intense anthropogenic pressure on the native media causing grave ecological problems such as deficiency of drinking water, shift of natural evolution of ecosystems due to species extinction, emphasizes the need of accurate analytical systems for continuous environmental monitoring. Microorganisms as simple sensitive living units conducting nutrient metabolic cycles in the environment are applicable for proper assessment of ambient media state. The paper will review modes of microbial contribution in indication and will list important and standard micro-indicators of water pollution. The article will describe up-to-date direct methods of pollutant detection and indirect indicator-recognition techniques. The peculiarities and requirements of water quality monitoring correlated with high dynamics and mobility of aqueous media will be discussed.