In the nuclear industry, large concrete pools are used for the short-term storage of spent fuel assemblies after their use in reactor. These structures can typically be up to 100 m in length and several tenth of meters in width. It is a regular practice to support them on soft pads that can simultaneously allow a free thermal expansion of the concrete and isolate the pool from possible seismic excitations. When subjected to seismic motion, both the structure and the contained fluid are dynamically excited, and a coupling exists between the two. The Housner model for fluid storage tank is often used in industrial studies to replace a direct representation of the fluid in the structural model of a pool. Analytical methods, such as those described in the Eurocodes allow a rough estimation of the wave height during an earthquake. In most cases though, the fluid is only represented by added masses acting normally to the pool walls. The present paper describes the building of a fully coupled fluid-structure Finite Element (FE) model of a seismically isolated storage pool and the lessons learned from it. The fluid is represented by acoustic elements with an explicit representation of the free surface sloshing modes. The adequacy of this model to capture wave heights during and after the earthquake is demonstrated by comparison with a full computational fluid dynamics (CFD) simulation. The combined effects of the seismic isolation system and the fluid-structure interaction are highlighted. The differences in results compared to the more standard approaches are illustrated.