Urban expansion leads to increasing water pollution, impacting both human health and ecosystems. This decline in water quality often stems from insufficient wastewater treatment, along with runoff from both urban and agricultural areas. Water quality degradation challenges our efforts for sustainable water management and hinders progress toward the UN's Sustainable Development Goals (SDGs), particularly SDG6. Within aquatic environments, the hyporheic zone—the subsurface area where surface water and groundwater mix—plays a crucial role in facilitating pollutant turnover and overall aquatic health. Mixing between surface water and groundwater generates diverse microhabitats in the streambed with varying levels of oxygen, temperature, and chemical composition, which in turn allows diverse microbial communities to strive. The complexity of exchange flows within the hyporheic zone and associated turnover processes of pollutants and nutrients can only be assessed with detailed, cross-disciplinary data sets including data about hydrology, climatology, biogeochemistry, and the subsurface composition. However, integrated data sets of this kind are seldom available. As a result, the drivers behind pollutant dynamics in stream-aquifer systems are still not fully understood. Addressing this knowledge deficit, we present a comprehensive unique data set from an urban stream-aquifer system in Switzerland spanning over 6 months. Incorporating hydrometric, tracer, nutrient, microbial and organic micropollutant data, our data set can help to shed light on the intricate mechanisms governing hyporheic exchange flows, as well as nutrient and organic micropollutant cycling in urban environments.