Achieving the UN Sustainable Development Goals depends on using resources efficiently, avoiding fragmentation in decision-making, recognising the trade-offs and synergies across sectors and adopting an integrated Nexus thinking among policymakers. Nexus Informatics develops the science of recognising and quantifying nexus interlinkages. Nexus-coherent solutions enhance the effect of policymaking in achieving adequate governance, leading to successful strategic vision and efficient resource management. In this article, we present the structure of a System Dynamics Model-the Nexus_SDM-that maps sector-specific data from major databases (e.g., EUROSTAT) and scenario models (e.g., E3ME-FTT OSeMOSYS and SWIM) for the national case study of Greece. Disaggregation algorithms are employed on annual national-scale data, turning them into detailed spatial and temporal datasets, by converting them to monthly values spread among all 14 River Basin Districts (RBDs). The Nexus_SDM calculates Nexus Interlinkage Factors and quantifies interlinkages among Water, Energy, Food, Built Environment, Natural Land and greenhouse gas (GHG) emissions. It simulates the nexus in the national case study of Greece as a holistic multi-sectoral system and provides insights into the vulnerability of resources to future socio-economic scenarios. It calculates the link between crop type/area, irrigation water and agricultural value, revealing which crops have the highest agricultural value with the least water and crop area. It demonstrates that fossil fuel power generation and use of oil for transportation are responsible for the most GHG emissions in most RBDs and presents projections for years 2030 and 2050. The analysis showcases that to move from a general nexus thinking to an operational nexus concept, it is important to focus on data availability and scale. Advanced Sankey and Chord diagrams are introduced to show distribution of resource use among RBDs and an innovative visualisation tool is developed, the Nexus Directional Chord plot, which reveals Nexus hotspots and strong interlinkages among sectors, facilitating stakeholder awareness.