The COVID-19 pandemic was a challenge for the whole world, and it had major secondary effects on humans and environmental health. The viral infection induced, in many situations, secondary bacterial infections, especially enteric infections, by destabilizing the balance of the gastrointestinal microbiota. The large-scale use of antibiotics and biocides for both curative and preventive purposes has resulted in an increase in bacterial resistance, and at the same time, the possibility of pathogenic microorganism multiplication and their dissemination to natural environments. Wastewater is the main vector of fecal microorganisms that favors their dissemination into natural aquatic ecosystems. The present paper aims to analyze the effect of the COVID-19 pandemic on the microbiological quality of wastewater from sewage treatment plants in Romania and its impact on receiving rivers. In order to highlight different and important areas in Romania, three cities from the east, center and west were selected for a microbiological evaluation of their WWTP influents and effluents from the pre-COVID-19 period and during the COVID-19 pandemic peak period, when the COVID-19 pandemic had a direct impact on WWTP microbial compositions. Our study shows that a higher level of contamination with fecal bacteria is linked to a higher COVID-19 incidence. The increased usage of pharmaceutical compounds, in turn, increases the number of resistant bacteria reaching the environment via WWTP effluents.