Agricultural policies are increasingly replaced by agro-environmental and rural-development polices. The rationale behind this evolution is that the policies seek to enhance the sustainability of agricultural systems and contributions from these systems to sustainable development at large. The same can be argued for agricultural innovations; they are increasingly aimed at serving a range of sustainability objectives, rather than only improving productivity and quality. As a result, resource use issues related to agriculture must be analysed and addressed from an integrated and multi-scale perspective. Both the introduction of alternative agricultural resource use options and agro-environmental policies would benefit from their ex ante assessment. Contributions from agronomy to such integrated assessment have strong implications for its research agenda. This chapter presents an extensive example of a multi-scale assessment methodology (SEAMLESS) in which agronomy plays a significant but partial role. The methods allow the investigation of different kinds of policies and innovations and their effects on economic, environmental and social objectives of stakeholders and decision makers at farm, regional and sector level.