This research explores the dynamic interplay of water, energy, and carbon in Axarquia, Spain (1990–2030), focusing on the escalating water deficit and rising emissions. It seeks to comprehend the impact of subtropical crop expansion on regional resources. A comprehensive methodology integrates data on water demand, alternative sources and energy-intensive processes. Key methods include assessing the influence of subtropical crops on water requirements by calculating the FAO 56 crop coefficient (Kc), the total annual energy (GWh) as a consequence of the volume of water demanded, identifying the predominant water sources and quantifying CO2 emissions by calculating the carbon footprint balance, providing a holistic view of regional resource dynamics. The methodology developed here can be adapted to basins elsewhere and can be a useful tool to help the design of water management policies in basins where the balance of the Water, Food, Energy nexus is of particular interest. The study reveals a substantial 30% surge in water demand due to exponential growth in subtropical crops. Additionally, energy-intensive processes linked to alternative water sources contribute to a projected surge in emissions (2022–2030), indicating significant regional challenges. Axarquia faces imminent challenges with a widening water deficit and escalating emissions. However, the region emerges as a vital carbon sink, evidenced by the net carbon balance. With 176,413 tCO2eq sequestered by cultivated plant mass, the study underscores the potential for environmental improvement and climate change mitigation in the region.