Humanity are facing grand challenges in food security and environmental sustainability under climate change and land-use intensification. To advance the understanding of the carbon-water-nutrients nexus at a granular level for broader agricultural area, a system approach is needed more than ever that can integrate both observational and modeling efforts. We invite submissions related with: (1) synthesis of multi-source observations over the agricultural ecosystem, including those from near-surface/airborne/satellite remote sensing, ground surveys, long-term agricultural experiments, and intensive sensor networks; (2) cross-scale process-based modeling of crop growth, management, environmental, and economic aspects of the agricultural system. The study domain can vary from whole-plant, field, farm, region, to the globe; (3) systematic model-data integration to support decision-making for improved farming practice, better policy design, and economic returns. We emphasize data-constrained modeling with reduced uncertainties, model-assisted sensor network design, and new cyberinfrastructure platforms and tools which can be readily adopted by stakeholders in decision-making.