Modeling of the spatial distribution of nitrogen transport and attenuation from various inland sources and along different hydrological pathways to coastal waters is needed for relevant decisions on effective allocation of measures for coastal nitrogen load abatement. We identify, classify, and quantify uncertainties associated with main discrepancies between spatial process representations in different catchment-scale nitrogen transport-attenuation models. The results show important model differences, indicating scientific disagreement on the realistic spatial process understanding, representation, and quantification in nitrogen transport-attenuation modeling. By further developing solutions for economic optimization of spatially differentiated nitrogen source abatement in coastal catchments, we find this disagreement to considerably affect the economic efficiency of coastal nitrogen load reduction. It may also lead to stakeholder mistrust and conflict and needs to be recognized and handled in environmental policy.