The COVID-19 pandemic reshaped the global response to a pandemic, including the way of using chemical compounds such as disinfectants and antibiotics. The large-scale use of antibiotics and disinfectants during the COVID-19 pandemic caused environmental pressure not only due to the chemicals themselves but also due to their effect on bacterial communities, inducing resistance to chemicals and changing the population structure of bacterial communities, especially in aquatic environments. The dissemination of fecal bacteria, including antibiotic-resistant bacteria, and pathogens from hospital wastewater into the environment, via wastewater treatment plants (WWTPs), triggered the premises of a major public health issue. Rivers flowing through cities are natural streams for WWTP discharges, and they directly bear the impact of anthropic activities, disseminating domestic and industrial pollution over large areas. The aim of the present study was to assess the microbiological bacterial structure of municipal and hospital wastewaters as well as their impact on natural streams, covering the pre-to post-COVID-19 pandemic period of time. The results indicated that the COVID-19 pandemic had a direct impact on hospital wastewater microbiological quality and the environment due to an excessive use of antibiotics and disinfectants. In addition, the constant presence of antibacterial compounds increased the rate of bacterial selection and induced population structural changes in the bacterial communities from aquatic systems.