The development of molecular technologies applied to environmental studies has shown that even in highly industrialized countries there is a high prevalence of viruses in the environment that represents an important impact on public health and substantial economic losses mainly related to the transmission of viruses through water and food. Significant concentrations of viruses are detected in the water flowed to the environment and in the biosolids generated in wastewater treatment plants. This work describes the general characteristics of the environmental contamination by viruses principally by emergent viruses, with a special emphasis on the hepatitis E virus (HEV) and the human polyomaviruses as the environmental contaminants more recently identified in industrialized countries. It has been shown that there is a high prevalence of the human polyomaviruses BKV and JCV in urban sewage in all studied countries, implying a potential transmission of these viruses and their potential oncogenic genes through the oral route. Recent studies have shown that the epidemiological pattern of the HEV infection in industrialized countries is complex and that a diversity of HEV strains simultaneously infects the population. The control of the viral contamination requires the standardization of molecular techniques and the development of a surveillance program for the evaluation of the viral parameters and to reduce the dissemination of already established diseases and emergent viral infections.