This study presents an innovative water-energy-food nexus (WEFN) generic multi-actor multi-level framework that simulates dynamic nexus systems and generates optimal resource management schemes and land-use allocation scenarios. The framework combines operational integrated multi-agent based simulations, dynamic agro-hydrological and renewable energy generation units (solar and wind) models and multi-criteria decision-making methods. It has been applied to a case study area of 800 km2 located downstream the Aveyron watershed, in Southwestern France. Local and regional strategic multi-criteria decision-making settings are compared. Under the local decision-making setting land-use allocation decisions are taken at agricultural parcel level whereas under the regional decision-making settings a single land allocation decision is taken for the whole territory. Possible land allocations are either crop rotations allocations, renewable energy generation units allocations or a mix of both. The framework is useful to generate scenarios of spatial allocations of renewable energy production units in an agricultural watershed facing water scarcity.