The suitability of acesulfame to trace wastewater-related surface water fluxes from streams into the hyporheic and riparian zones over long-term periods was investigated. The transport behavior of acesulfame was compared with the transport of water stable isotopes (δ18O or δ2H). A calibrated model based on a joint inversion of temperature, acesulfame, and piezometric pressure heads was employed in a model validation using data sets of acesulfame and water stable isotopes collected over 5 months in a stream and groundwater. The spatial distribution of fresh water within the groundwater resulting from surface water infiltration was estimated by computing groundwater ages and compared with the predicted acesulfame plume obtained after 153 day simulation time. Both, surface water ratios calculated with a mixing equation from water stable isotopes and simulated acesulfame mass fluxes, were investigated for their ability to estimate the contribution of wastewater-related surface water inflow within groundwater. The results of this study point to limitations for the application of acesulfame to trace surface water–groundwater interactions properly. Acesulfame completely missed the wastewater-related surface water volumes that still remained in the hyporheic zone under stream-gaining conditions. In contrast, under stream-losing conditions, which developed after periods of stagnating hydraulic exchange, acesulfame based predictions lead to an overestimation of the surface water volume of up to 25% in the riparian zone. If slow seepage velocities prevail a proportion of acesulfame might be stored in smaller pores, while when released under fast flowing water conditions it will travel further downstream with the groundwater flow direction. Therefore, under such conditions acesulfame can be a less-ideal tracer in the hyporheic and riparian zones and additional monitoring with other environmental tracers such as water stable isotopes is highly recommended.