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Microbial contamination of urban water is a global concern for public health safety particularly in developing countries. Microorganisms like bacteria (Salmonella, Shigella, Vibrio cholera), viruses (Rotavirus, Norovirus), protozoa (Giardia and Cryptosporidium) and blue green algae (Nostoc) are prevalent pathogens of drinking water. Blue green algae form algal blooms and secret toxic compounds (such as cyanotoxins) in water bodies. The main sources of pathogens in water are due to fecal matter of livestock and wildlife, sewage water and effluent of industrial/pharmaceutical plants. Poor management and unawareness cause water-borne diseases in humans due to consumption of contaminated drinking water. This chapter provides a brief overview of classical and advanced analytical techniques for biological micropollutants detection in contaminated waters. Further, the techniques such as membrane filtration …