Since the COVID-19 pandemic, wastewater monitoring has become an additional tool in the surveillance of infectious diseases. Many EU countries put wastewater surveillance systems (WSS) in place to track SARS-CoV-2 and its variants and other pathogens, such as the influenza virus or Respiratory syncytial virus (RSV). In Germany, several research and pilot projects funded by the EU, the Federal Ministry of Education and Research, the Federal Ministry of Health, and projects at Federal State level have been launched in the last four years. In Germany, wastewater monitoring was not implemented as a public health tool before the COVID-19 pandemic, but in September 2022, it has been legally determined in the German infection protection act (Infektionsschutzgesetz, IfSG). As Germany is a federal state, competencies in epidemic management partly belong to the 16 federal states (“Länder”). In the federal states, the local health authorities at the county (“Kreise”) level also have specific risk management and communication competencies. Furthermore, WSS has been incorporated into the revised Urban Wastewater Treatment Directive (EU) 2024/3019. For this reason, the federal states and local health authorities play a pivotal role in successfully implementing wastewater monitoring as a supplementary component of disease surveillance in Germany. Between November 2021 and August 2022, the federal state of Thuringia, Germany, supported a pilot study to implement a surveillance system for SARS-CoV-2-RNA in wastewater of 23 wastewater treatment plants in 17 counties in Thuringia. Here, we describe the study design and the system behind the logistics and the planning, and we provide an overview of the options for involving the public health service. Furthermore, the possibilities for IT concepts and approaches to innovative AI solutions are shown. We also aim to explore the feasibility and potential barriers to further implementing wastewater surveillance as a supplementary public health tool in Thuringia.