The water-energy-food (WEF) nexus concept highlights the importance of integrative solutions that secure resource supplies and meet demands sustainably. There is a need for translating the nexus concept into clear frameworks and tools that can be applied to decision making. A simulation and analytics framework, and a concomitant Nexus Simulation System (NexSym) is presented here. NexSym advances the state-of-the-art in nexus tools by explicit dynamic modelling of local techno-ecological interactions relevant to WEF operations. The modular tool integrates models for ecosystems, WEF production and consumption components and allows the user to build, simulate and analyse a "flowsheet" of a local system. This enables elucidation of critical interactions and gaining knowledge and understanding that supports innovative solutions by balancing resource supply and demand and increasing synergies between components, while maintaining ecosystems. NexSym allowed assessment of the synergistic design of a local nexus system in a UK eco-town. The design improved local nutrient balance and meets 100% of electricity demand, while achieving higher carbon capture and biomass provisioning, higher water reuse and food production, however with a remarkable impact on land use.