While topology optimization (TO) is widely used in aerospace engineering to achieve lightweight, high-performance structures, its application in naval architecture remains limited due to the complexity of fluid–structure interaction and design-dependent loading. This work presents a computational framework for the structural topology optimization of floating structures subjected to hydroelastic forces, aiming to minimize compliance under a volume constraint. The method is based on the Topology Optimization of Binary Structures with Geometry Trimming (TOBS-GT), which performs geometry trimming prior to finite-element analysis (FEA), enabling an accurate and explicit representation of structural boundaries and fluid–structure interfaces. The framework is implemented in MATLAB and coupled with COMSOL Multiphysics, explicitly accounting for design-dependent hydrostatic pressure loads. A key result is that, in this formulation, hydrostatic pressure acting on external boundaries does not require interpolation for sensitivity analysis, whereas structural self-weight must be interpolated to ensure consistent and accurate optimization gradients. The approach is demonstrated on a three-dimensional box-shaped floating structure subjected to multiple loading conditions, including still water, hogging, and sagging induced by linear waves. The optimized design achieves a 35% increase in stiffness relative to a conventional grid-based baseline at equal material volume. To bridge numerical and physical validation, the design is being tested in a wave tank at TU Delft using 3D-printed PET-G models manufactured with a perimeter-based printing strategy to ensure watertightness and near-isotropic mechanical behavior. The results demonstrate that topology optimization can be extended to hydroelastic naval structures, enabling lighter and more efficient floating designs.