According to the concept of ecosystem services, agriculture not only provides commodities but also cultural and regulating services. While it is easy to value commodity production by market prices, the valuation of cultural and regulating services is complex because of their public good character. Non-parametric approaches such as the Data Envelopment Analysis (DEA) allow for estimating the contribution of agriculture to such services. However, it is not enough to know the extent of ecosystem services provided; it is also necessary to be aware of which farmers provide these services and where they are provided. In this paper, we suggest a plot-specific approach combining GIS analysis and DEA models. This allows a spatially explicit assessment of agricultural land use for different subject matters such as ecology and the contribution of a single plot to landscape diversity. The approach is undertaken in a marginal low-mountain region in Germany on 95 farms involving more than 5,800 plots. The results show the spatial distribution of externalities supplied by agriculture and the degree of segregation between “production areas” and “protection areas”. The results also allow a deeper understanding of the spatial impact of policy measures on the provision of ecosystem services by agriculture.