The contamination of waters with nutrients, especially nitrogen and phosphorus originating from various diffuse and point sources, has become a worldwide issue in recent decades. Due to the complexity of the processes involved, watershed models are gaining an increasing role in their analysis. The goal set by the EU Water Framework Directive (to reach “good status” of all water bodies) requires spatially detailed information on the fate of contaminants. In this study, the watershed nutrient model MONERIS was applied to the Hungarian part of the Danube River Basin. The spatial resolution was 1078 water bodies (mean area of 86 km²); two subsequent 4 year periods (2009–2012 and 2013–2016) were modeled. Various elements/parameters of the model were adjusted and tested against surface and subsurface water quality measurements conducted all over the country, namely (i) the water balance equations (surface and subsurface runoff), (ii) the nitrogen retention parameters of the subsurface pathways (excluding tile drainage), (iii) the shallow groundwater phosphorus concentrations, and (iv) the surface water retention parameters. The study revealed that (i) digital-filter-based separation of surface and subsurface runoff yielded different values of these components, but this change did not influence nutrient loads significantly; (ii) shallow groundwater phosphorus concentrations in the sandy soils of Hungary differ from those of the MONERIS default values; (iii) a significant change of the phosphorus in-stream retention parameters was needed to approach measured in-stream phosphorus load values. Local emissions and pathways were analyzed and compared with previous model results.