Water quality can be defined as a measurement of a water’s appropriateness for a specific purpose based on biological, chemical, and physical qualities. Water pollution caused by microorganisms is one of the most serious threats to the aquatic ecosystem around the world. The bacterial concentration in an aquatic environment is raised by anthropogenic activities and industrial-agricultural pollutants. Coliform bacteria have long been used as an indicator organism for microbial pollution of water, which has contributed to potential health risks. Escherichia coli is the coliform that indicates fecal contamination. Various methods such as culture-dependent methods, culture-independent gene sequence-based methods, and immunological methods are used to determine bacterial contamination in water sources. As a consequence, determining that the water is not suitable for use by bacteriological analysis indicates that the water is contaminated. This chapter highlights the sanitary quality of aquatic environments, indicator organisms for water quality assessment, detection of bacterial pollution in the water source, and bacterial waterborne diseases.