The hydraulics of water and wastewater treatment reactors has a major impact on their performance and control. The residence time distribution as a measure for the hydraulics represents macroscopic mixing in an integrated way with no spatial information. However, with regard to optimal sensor location for process control and for process optimisation measures, spatial information about macro-mixing is helpful. Spatially distributed measurements of reactive tracers can provide this information. In this paper we generally discuss how reactive tracers can be used to detect and characterize distinct large scale flow structures. It is shown that tracer substances are particularly suited if their reaction time scale is similar to the time scale of the large scale flow structure. For nitrifying activated sludge systems, ammonium is identified to be a suitable tracer. In a comprehensive experimental study at a real aeration tank, two distinct large scale flow features were identified by distributed ammonium measurements. Flow velocity measurements using acoustic Doppler velocimetry clearly supported the nature of these flow field anomalies. Ion selective electrodes are a well suited device for ammonium measurements providing the temporal resolution that is needed for such an analysis.