This study investigated the three-dimensional flow structures in an ellipsoid, closed sea fish cage. The results are presented using computational fluid dynamics (CFD) simulations and experimental measurements. Experimental residence time distribution (RTD) measurement and CFD simulation are the best methods to study the hydrodynamics of inflow systems. Three-dimensional numerical simulations of the flow and transport characteristics of the system were conducted using a Reynolds-averaged Navier-Stokes equation approach and the results were compared to the measurements performed using acoustic Doppler velocimetry techniques. The objective of the investigation was to characterize the flow field generated in an ellipsoid, closed tank. The flow in the enclosed volume is driven by four inlets pipes integrated into the wall of the cage. The focus is on the turbulent structures and undesirable flow patterns that lead to reduced self-cleaning efficiency and a lower quality habitat for the fish through phenomena, such as recirculation zones or low velocity areas. Correlations between CFD and the experimental data confirm the adequate reproduction of hydrodynamic conditions and reinforce the predictive capabilities of numerical models as tools to simulate field scale closed containment systems or to optimize existing and future aquaculture designs. The simulation of aquaculture-like particles demonstrates that almost 100% of particles with a diameter ranging between 1 μm and 3000 μm are removed during a maximum of two hydraulic retention time (HRT) cycles. Smaller particles are removed via the upper-side outlets and larger particles are removed via the bottom outlet.