Two Austrian case study regions within the Danube basin have been selected for detailed investigations of groundwater and surface water quality at the catchment scale. Water balance calculations have been performed using the conceptual continuous time SWAT 2000 model to characterise catchment hydrology and to identify individual runoff components contributing to river discharge. Nitrogen emission calculations have been performed using the empirical emission model MONERIS to relate individual runoff components to specific nitrogen emissions and for the quantification of total nitrogen emissions to surface waters. Calculated total nitrogen emissions to surface waters using the MONERIS model were significantly influenced by hydrological conditions. For both catchments the groundwater could be identified as major emission pathway of nitrogen emissions to the surface waters. Since most of the nitrogen is emitted by groundwater to the surface water, denitrification in groundwater is of considerable importance reducing nitrogen levels in groundwater along the flow path towards the surface water. An approach was adopted for the grid-oriented estimation of diffuse nitrogen emissions based on calculated groundwater residence time distributions. Denitrification in groundwater was considered using a half life time approach. It could be shown that more than 90% of the total diffuse nitrogen emissions were contributed by areas with low groundwater residence times and short distances to the surface water. Thus, managing diffuse nitrogen emissions the location of catchment areas has to be considered as well as hydrological and hydrogeological conditions, which significantly influence denitrification in the groundwater and reduce nitrogen levels in groundwater on the flow path towards the surface water.

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