The new water quality protection approach of the EU combines the control of emissions with instream Environmental Quality Standards (=EQS). Since 1 April 2006 and actually relevant in the version of 2010 in Austria, priority substances from list A of the EUROPEAN DIERECTIVE 76/464 and further EQS of relevant chemical substances (list B), identified by a national risk assessment, have to be reached to achieve a good ecological state in the surface water (Edict for Water Quality Standards, 2006; changes to the Edict for Water Quality Standards 2010). The practical assessment of these substances after point source emissions is prescribed in the Edict, but rarely carried out. In this paper, two substances, namely: (1) ammonium (list B); and (2) nonylphenol, an endocrine disrupting compound (list A) are presented to discuss: (i) the improvement of treatment efficiency due to the upgrade of a large Waste Water Treatment Plant (=WWTP); (ii) the relevance of mixing processes and modelling as a method to control EQS after point source emissions; and (iii) the improvement of water quality in the ambient surface waters. It is shown that the improved treatment in the case of nonylphenol leads to emission values which fall below the EQS, making an assessment unnecessary. In the case of ammonium emission, values are significantly reduced and violation of EQS is avoided, while mixing modelling is shown to be a suitable instrument to address the resulting instream concentrations at different border conditions.