Agricultural systems are becoming increasingly complex, requiring data-driven, science-supported models to address their multifaceted challenges and ensure sustainable management. In Greece, agriculture is a critical sector, contributing significantly to the economy and rural livelihoods, but it also faces pressing challenges such as competing water uses, energy demands, lackluster productivity, and environmental pressures. This study presents a comprehensive multi-model assessment of Greece’s Water–Energy–Food–Ecosystems Nexus, evaluating agricultural production alongside energy and water requirements and quantifying the associated air pollution impacts at the national level. For the first time to our knowledge, we connect the FABLE Calculator (the software of the FABLE Consortium) with LEAP (Low Emissions Analysis Platform, from the Stockholm Environmental Institute) and the WaterReqGCH (a model developed by the Global Climate Hub). The FABLE Calculator provides detailed estimates of agricultural and livestock production, which are then used by LEAP to calculate the respective energy demand and the associated greenhouse gas emissions per fuel type used. The WaterReqGCH model uses the activity levels in FABLE and LEAP in order to estimate the water requirements of the agricultural and livestock sector. The models run based on a current accounts scenario expressing Greece's national commitments to the agri-food, energy, and water sectors according to the Greek Common Agricultural Policy (CAP) Plan, the National Energy and Climate Plan (NECP), and the River Basin Management Plans. The results indicate that the implementation of the CAP Plan, combining higher productivity, together with the NECP, assuming cleaner fuels, can result in a 73.4% decline in Greece's agricultural production GHG emissions despite the slight increase in the sector's energy consumption by 15% in 2050. Agriculture is the dominant consumer of water resources, consistently accounting for 88–89% of the total water consumption over the period 2020-2050. Agricultural water consumption follows a slight increase after 2025 and reaches an average consumption of 8041.12hm³ by 2050, with only minor fluctuations and large uncertainty ranges due to a combination of hydro-climatic and agronomic parameters. The assumed higher productivity of the agricultural sector is likely to also increase its total water consumption. The insights provided by this multi-model approach are useful and holistic evidence for policymaking, highlighting the need for more coordinated approaches.