Egypt’s agricultural sector confronts compounding pressures from water scarcity, soil salinisation, and rapid urbanisation. Decoupled recirculating aquaponic systems (DRAPS) represent a promising response, integrating independent fish and plant production loops with IoT-enabled monitoring to achieve substantial reductions in water and land demand. This study presents a 24-month performance and economic assessment of a 400 m² DRAPS pilot greenhouse at the Egyptian Chinese University (ECU), Cairo, operating under real arid-climate conditions as part of the EU PRIMA Mara–Mediterra project. Water quality parameters, including pH in both the aquaculture and hydroponic loops, total dissolved solids (TDS) and greenhouse temperature were logged continuously. A crop-by-crop techno-economic analysis covering seven vegetable crops and Nile tilapia (Oreochromis niloticus) was conducted using net present value, internal rate of return, and payback period across a 5-year horizon. The results show that five of seven crops are economically viable at a 20% discount rate, with Red Batavia achieving the highest net present value (NPV) (323,863 EGP) and IRR (59.55%) and a payback period of 1.5 years. A scenario analysis projects that scaling to a four-unit, 1600 m² cluster could raise IRR to approximately 62% through a reduction in capital expenditure from economies of scale, while delivering annual water savings of 1.9 million litres relative to conventional soil-based agriculture. These findings demonstrate that IoT-integrated DRAPS is both technically viable and financially attractive for commercial-scale deployment in water-scarce arid regions.