High spatial and temporal resolution monitoring systems are needed to improve our knowledge on flow and matter transport pathways and substance transformation. The presentation will introduce a new online water quality monitoring system as part of the UFZ TERENO Hydrological Observatory “Bode” and show how this new information can improve river water quality modelling. Additional low flow measurement campaigns including delta 18O and delta 15N isotope analyses of nitrate have been used to identify denitrification processes on a selected lower river reach. It will be demonstrated how high resolution data can be used in combination with a process based river water quality model (Boyacioglu et al. 2011) to improve model identification. The multi objective calibration helps in combination with cross validation to assess the information content of the data (Rode et al 2007). It is explained how a sound monitoring concept can be used in combination with process-based river water quality modelling to improve our knowledge on in-stream nutrient retention.