Human activities severely affect aquatic ecosystems: the lockdown restrictions due to SARS-CoV-2 (COVID-19) have proved that reducing anthropogenic activities can positively influence the environment and mitigate atmospheric pollution. In addition, studies on aquatic ecosystems have highlighted the decrease in suspended matter and pollutant concentrations associated with reduced marine transport and industrial activities. We evaluated the effects of the reduction of anthropogenic activities in highly impacted water ecosystems. Three of the sampling sites were on the Tiber River's lower stretch close to the urban area of Rome (Italy), and the other two were transitional waters located in the southern Latium region coastal area. These sampling sites have been studied by our research group for at least 20 years. The present study involved analysis of chemical and physicochemical parameters, biological communities, and land use. Microbiological fecal indicators and Salmonella spp. were also analyzed. There were two sampling campaigns, the first one in May 2020 (ID II) at the end of lockdown measures, and the second one a year later, in June 2021 (ID III). The data were compared with our old data, collected from 2002 to 2015 (ID I), to evaluate the potential effects of the restrictive measures. Biotic communities were dominated by pollution-tolerant taxa, indicating eutrophication and organic pollution. Furthermore, the high concentrations of microbiological indicators was mainly due to sewage from the urban area. The results of the research indicated no significant changes from past years (ID I) to 2020 (ID II) and 2021 (ID III). In conclusion, the restrictions adopted in Italy during the pandemic period were not sufficient to mitigate the heavy pressure of urbanization and agriculture that have long affected the studied aquatic ecosystems. Environ Toxicol Chem 2023;42:966-977. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.