Preservation of urban aquatic ecosystems is of primary importance for human well-being, biodiversity protection and the future of society. Lake–groundwater–river interactions within urban floodplains harbour intrinsic fragility, yet remain largely understudied. Appropriate environmental management can help assure the conservation of these sites through strategies that are based on physical, chemical and isotope constraints. Here we present the example of the Groundwater and Lakes Urban Observatory (GLUO) in Magdeburg, Germany, where monitoring has been carried out since 2022. Our database for the year 2023 includes data from the Elbe River, two lakes named Lake Salbker South and Lake Salbker North, and two groundwater wells. Major ion patterns point to the Elbe River and Lake Salbker South as the end-members for water compositions within the system, although contributions from the former appear less significant. Stiff plots suggest the existence of a more saline end-member that may receive inputs from the Zechstein Formation and drives the geochemistry of Lake Salbker South. Dissolved oxygen (DO) concentrations in Lake Salbker South during stratification show a marked depletion in the hypolimnion with values down to 1.8 mg L⁻¹ that we attribute to mineralization of organic matter as well as oxidation of sulphur compounds. This feature acknowledges Lake Salbker South as a natural hydrogen sulphide (H₂S) reactor. Water stable isotope compositions (δ²H_H2O and δ¹⁸O_H2O) of the water bodies within the GLUO outline a trend that is compatible with moderate evaporation. We discuss that dissolution of saline deposits may also play a role. These findings emphasize the need to implement the study of lake–groundwater–river interactions within floodplains, especially when hypertrophic or sulphur-rich water bodies are involved. Due to the inherent vulnerability and potential hazards associated to these environments, we stress the importance of establishing a multidisciplinary monitoring framework to evaluate their geochemical fluxes and ecological integrity.