This research addressed the study of water, energy, and mass transport phenomena in a sustainable bio – integrated Recirculating Aquaponic System (RAS) coupling the growth of Oncorhynchus mykiss (rainbow trout) and Lactuca sativa (lettuce). The hypothesis proposed that the energy–environmental sustainability of such sub-systems improves when the transport of fluids, heat, and matter within the production cycle is known, characterized, and modeled; and that integrating engineering, biology, and aquaculture knowledge enhances productivity and product quality while enabling predictive scaling. To test these hypotheses, the study was developed in three stages. First, an exhaustive bibliographic review and experimental characterization of the prototype were performed to quantify the environmental conditions, growth dynamics, and physicochemical variability of each specie throughout the production cycle. Experimental measurements included hydraulic flow rate, dissolved oxygen, pH, temperature, and nitrogen compounds (NH4+, NO2−, NO3−). These data established the operational baselines and environmental constraints of the system. In the second stage, a physic–biological–mathematical model was formulated to describe the coupled processes of hydrodynamics, heat transfer, and biochemical transformations. The model was derived from the conservation equations of mass, momentum, and energy. The system of partial differential equations described the coupled behavior of water flow, heat transfer, and nutrient dynamics in the aquaponic system. This model was implemented in ANSYS Fluent using CFD and the finite volume method, with a 3D geometry based on the experimental setup. Steady and transient simulations were carried out to predict velocity patterns, temperature distribution, and spatial variations of oxygen and nitrogen species. This research contributed to gain original insights into the quantitative understanding of transport processes in aquaponics, providing a predictive and scalable framework for designing sustainable aquaculture– hydroponic production systems that minimize environmental impacts and maximize resource efficiency.