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Introduction Molecular studies have confirmed the silent circulation of enterovirus (EntV) and hepatitis A virus in the environment, even in the absence of clinical manifestation. Viral pathogens are among the major causes of disease outbreaks, particularly in the bigger cities and both in the developed and underdeveloped nations. Material and methods Between June 2016 – June 2017, 97 samples of drinking water, river water polluted with sewage and blood were selected and obtained from high risk communities in Pakistan. Negatively charged membrane filters were used to concentrate the virus, followed by the use of specific PCR primers set for quick identification of the waterborne viruses. Results Enteroviruses were recovered from 40%, 28.57% and 33.33% of river water polluted with sewage samples in Lahore, Islamabad and Rawalpindi, respectively, while the presence of 13.13% and 11.76% of viral load was also confirmed in the drinking water of Lahore and Rawalpindi, respectively. A high prevalence of HAV (12.5% and 21.05%) was also verified in the clinical samples. Phylogenetic analysis indicated close resemblance of HAV isolates with the Indian strains. This study is the first ever comparative analysis of the EntV and HAV isolated from environmental samples and clinical specimen on a molecular level. Conclusions The parallel surveillance of EntV and HAV in the river water polluted with sewage, and clinical samples is quite helpful for controlling and reducing the disease burden of the waterborne illnesses.