AbstractThe 2 ha pilot‐plant Seawater Energy and Agriculture System (SEAS) in Abu Dhabi, United Arab Emirates (UAE), integrates aquaculture ponds, which produce fish and shrimp, with fields of Salicornia and mangrove used as a natural filter to clean the waste seawater from the ponds. The SEAS is a sustainable solution that addresses the food security issues of countries with large deserts or arid regions. At the same time, it produces economically viable fuels from biomass, using non‐arable lands and non‐drinkable water. After harvesting and pressing Salicornia seeds (2 t ha−1 year−1), a custom‐made process serves to pre‐treat the vegetable oil (0.7 t ha−1 year−1) containing 85 wt% C18 and 10 wt% C16 fatty acids as triglycerides. The first step of the UOP Ecofining® process produces an oil composed of linear C15‐C18 alkanes. Analytical data suggest the oil feed converts at 60 wt% by hydrodeoxygenation and at 40 wt% through decarboxylation/decarbonylation. The subsequent hydrocracking/isomerization step provided 3.4 wt% C1–C4, 34.8 wt% green naphtha, 47.5 wt% sustainable aviation fuel (SAF), and 14.2 wt% green diesel. After distillation, the SAF has been certified following ASTM D7566 before being blended with conventional jet fuel and used successfully on a commercial passenger flight in January 2019. The techno‐economic study shows that the biorefinery part is economically sustainable when reaching a production scale of 900bbd, required for a SEAS surface of 20 000 ha. At this scale, expected revenue and conversion costs per MT of feed are, respectively, $589 and $290. The resulting benefit, associated with a CAPEX of $115M, would lead to a payback time of 6.9 years. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd