Water is the most precious gift of nature to humanity. Safe drinking water is essential to humans and other live forms. Microbial contamination of drinking water by pathogens contained in human or animal excreta has the potential to cause large outbreaks of waterborne diseases. Although contaminated water causes serious problem in most population of the world, communities in developing countries suffer markedly due to lack of safe and sanitary water supply and disposal systems. Recognizing waterborne diseases resulting from natural, accidental or intentional contamination of water supplies is a diagnostic challenge for the medical personnel due to difficulties in detecting microbial pathogens. Accurate and timely diagnosis of these diseases is a critical element to any successful strategy to protect water quality and security and ultimately the public health. This document discusses all aspects related to microbiology of drinking water based on personal works and research findings during the last few decades.