<p>This study evaluated the performance of coupled aquaponic systems, based on a floating raft configuration (deep water culture, DWC), for the cultivation of high-value fruit crops and red tilapia (<i>Oreochromis</i> sp.) under tropical greenhouse conditions. In phase 1, a 2 × 2 factorial design was implemented to assess the effects of two fish stocking densities (114 and 171 fish·m⁻³) and two hydraulic loading rates (6 and 12 m³·m⁻²·day⁻¹) on the production of serrano pepper (Capsicum annuum). In phase 2, the most efficient aquaponic configuration from phase 1 was applied to tomato (<i>Solanum lycopersicum</i>) and cucumber (<i>Cucumis sativus</i>) and compared to hydroponic controls. Water quality remained within optimal ranges across treatments, while plant and fish performance were significantly influenced by stocking density and HLR. The aquaponic treatment with 114 fish·m⁻³ and 12 m³·m⁻²·day⁻¹ produced the best overall results in phase 1. In phase 2, cucumber outperformed tomato in terms of yield, and both aquaponic crops exceeded the productivity of hydroponic controls. Hematological, immunological, and hormonal indicators revealed better physiological status in fish reared under moderate-density aquaponic conditions. The System Efficiency Index (SEI) confirmed that properly balanced aquaponic systems can optimize biological performance and resource use. These findings support the viability of floating raft aquaponics as a sustainable alternative to conventional soilless systems in tropical environments.</p>