Traditional agricultural systems and their spatial context constitute socio-ecological landscapes for their long co-evolutionary history. However, these systems not only generate positive but also negative agri-environmental externalities, such as soil erosion, diffuse pollution and potential wild biodiversity degradation. In this paper, we present a methodological approach for developing and testing indicators to estimate the effects of these externalities, especially designed to be used to help guide land-use policy changes. Our results show that the indicators proposed can recognize the different environmental situations posed by the three selected study areas, in terms of potential erosion and diffuse pollution, as well as in the actual agri-environmental externalities assessment. As expected, they also respond to the changes in land use and management introduced by two scenarios, ecological and productive. Although the erosion and diffuse pollution indicators showed a linear response, the diversity indicator showed a non-linear response, which highlights the importance of the spatial structure of landscape in agri-environmental assessment. In fact, several ecological processes can be affected by landscape spatial structure, potentially giving unexpected results both in terms of indicators and of real impact of agri-environmental externalities. Therefore, some landscape structure assessment should accompany that of externalities when considering land-use policy objectives.