Viruses and phages in water and the solid compartments undergo inactivation by both natural and human-introduced physical, chemical, and biological stressors. In primary sedimentation, flocculation-aided sedimentation, activated sludge digestion, activated sludge digestion plus precipitation, and upflow anaerobic sludge blanket processes, the die-off of the microorganisms seems to play a minor role in the reduction in counts. Viruses and bacteriophages persist longer than conventional bacterial indicators in water environments, and their persistence resembles that of viruses, as shown by model experiments and by the decreases in ratios between the numbers of conventional bacterial indicators and of viruses and phages in water environments with aged pollutants, either surface water. Bacteriophages infecting enteric bacteria have been reported in drinking water that fulfill the quality criteria based on bacterial indicators. Most likely, the application of advanced mathematical models such as artificial neural networks or support vector machines will reduce the uncertainty and give much better information about relationships between indicator bacteriophages and human viruses. In conclusion, it can be stated that, though not perfect, bacteriophages infecting enteric bacteria are useful additional indicators for water quality control because of their numbers in fecally contaminated water and their outcome in water environments and water treatment plants.